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| <?xml version="1.0" encoding="UTF-8"?><!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.1d1 20130915//EN" "JATS-archivearticle1.dtd"><article article-type="research-article" dtd-version="1.1d1" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><front><journal-meta><journal-id journal-id-type="nlm-ta">elife</journal-id><journal-id journal-id-type="hwp">eLife</journal-id><journal-id journal-id-type="publisher-id">eLife</journal-id><journal-title-group><journal-title>eLife</journal-title></journal-title-group><issn publication-format="electronic">2050-084X</issn><publisher><publisher-name>eLife Sciences Publications, Ltd</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="publisher-id">03430</article-id><article-id pub-id-type="doi">10.7554/eLife.03430</article-id><article-categories><subj-group subj-group-type="display-channel"><subject>Research article</subject></subj-group><subj-group subj-group-type="heading"><subject>Genomics and evolutionary biology</subject></subj-group></article-categories><title-group><article-title>Sequence co-evolution gives 3D contacts and structures of protein complexes</article-title></title-group><contrib-group><contrib contrib-type="author" equal-contrib="yes" id="author-14388"><name><surname>Hopf</surname><given-names>Thomas A</given-names></name><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0002-7476-9539</contrib-id><xref ref-type="aff" rid="aff1"/><xref ref-type="aff" rid="aff2"/><xref ref-type="fn" rid="equal-contrib">†</xref><xref ref-type="other" rid="par-1"/><xref ref-type="fn" rid="con1"/><xref ref-type="fn" rid="conf1"/><xref ref-type="other" rid="dataro1"/></contrib><contrib contrib-type="author" equal-contrib="yes" id="author-14389"><name><surname>Schärfe</surname><given-names>Charlotta P I</given-names></name><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0002-6689-6423</contrib-id><xref ref-type="aff" rid="aff1"/><xref ref-type="aff" rid="aff3"/><xref ref-type="aff" rid="aff4"/><xref ref-type="fn" rid="equal-contrib">†</xref><xref ref-type="other" rid="par-2"/><xref ref-type="fn" rid="con2"/><xref ref-type="fn" rid="conf1"/><xref ref-type="other" rid="dataro1"/></contrib><contrib contrib-type="author" equal-contrib="yes" id="author-14390"><name><surname>Rodrigues</surname><given-names>João P G L M</given-names></name><xref ref-type="aff" rid="aff5"/><xref ref-type="fn" rid="equal-contrib">†</xref><xref ref-type="fn" rid="con4"/><xref ref-type="fn" rid="conf1"/><xref ref-type="other" rid="dataro1"/></contrib><contrib contrib-type="author" id="author-14391"><name><surname>Green</surname><given-names>Anna G</given-names></name><xref ref-type="aff" rid="aff1"/><xref ref-type="fn" rid="con5"/><xref ref-type="fn" rid="conf1"/><xref ref-type="other" rid="dataro1"/></contrib><contrib contrib-type="author" id="author-19310"><name><surname>Kohlbacher</surname><given-names>Oliver</given-names></name><xref ref-type="aff" rid="aff3"/><xref ref-type="aff" rid="aff4"/><xref ref-type="fn" rid="con6"/><xref ref-type="fn" rid="conf1"/></contrib><contrib contrib-type="author" corresp="yes" id="author-14392"><name><surname>Sander</surname><given-names>Chris</given-names></name><xref ref-type="aff" rid="aff6"/><xref ref-type="corresp" rid="cor1">*</xref><xref ref-type="other" rid="par-1"/><xref ref-type="fn" rid="con7"/><xref ref-type="fn" rid="conf1"/><xref ref-type="other" rid="dataro1"/></contrib><contrib contrib-type="author" corresp="yes" id="author-4602"><name><surname>Bonvin</surname><given-names>Alexandre M J J</given-names></name><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0001-7369-1322</contrib-id><xref ref-type="aff" rid="aff5"/><xref ref-type="corresp" rid="cor2">*</xref><xref ref-type="fn" rid="con8"/><xref ref-type="fn" rid="conf1"/><xref ref-type="other" rid="dataro1"/></contrib><contrib contrib-type="author" corresp="yes" id="author-14168"><name><surname>Marks</surname><given-names>Debora S</given-names></name><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0001-9388-2281</contrib-id><xref ref-type="aff" rid="aff1"/><xref ref-type="corresp" rid="cor3">*</xref><xref ref-type="other" rid="par-1"/><xref ref-type="fn" rid="con3"/><xref ref-type="fn" rid="conf1"/><xref ref-type="other" rid="dataro1"/></contrib><aff id="aff1"><institution content-type="dept">Department of Systems Biology</institution>, <institution>Harvard University</institution>, <addr-line><named-content content-type="city">Boston</named-content></addr-line>, <country>United States</country></aff><aff id="aff2"><institution content-type="dept">Bioinformatics and Computational Biology, Department of Informatics</institution>, <institution>Technische Universität München</institution>, <addr-line><named-content content-type="city">Garching</named-content></addr-line>, <country>Germany</country></aff><aff id="aff3"><institution content-type="dept">Applied Bioinformatics, Quantitative Biology Center</institution>, <institution>University of Tübingen</institution>, <addr-line><named-content content-type="city">Tübingen</named-content></addr-line>, <country>Germany</country></aff><aff id="aff4"><institution content-type="dept">Department of Computer Science</institution>, <institution>University of Tübingen</institution>, <addr-line><named-content content-type="city">Tübingen</named-content></addr-line>, <country>Germany</country></aff><aff id="aff5"><institution content-type="dept">Computational Structural Biology Group</institution>, <institution>Bijvoet Center for Biomolecular Research, Utrecht University</institution>, <addr-line><named-content content-type="city">Utrecht</named-content></addr-line>, <country>Netherlands</country></aff><aff id="aff6"><institution content-type="dept">Computational Biology Center</institution>, <institution>Memorial Sloan Kettering Cancer Center</institution>, <addr-line><named-content content-type="city">New York</named-content></addr-line>, <country>United States</country></aff></contrib-group><contrib-group content-type="section"><contrib contrib-type="editor"><name><surname>Kuriyan</surname><given-names>John</given-names></name><role>Reviewing editor</role><aff><institution>Howard Hughes Medical Institute, University of California, Berkeley</institution>, <country>United States</country></aff></contrib></contrib-group><author-notes><corresp id="cor1"><label>*</label>For correspondence: <email>sander@cbio.mskcc.org</email> (CS);</corresp><corresp id="cor2"><label>*</label>For correspondence: <email>a.m.j.j.bonvin@uu.nl</email> (AMJJB);</corresp><corresp id="cor3"><label>*</label>For correspondence: <email>debbie@hms.harvard.edu</email> (DSM)</corresp><fn fn-type="con" id="equal-contrib"><label>†</label><p>These authors contributed equally to this work</p></fn></author-notes><pub-date date-type="pub" publication-format="electronic"><day>25</day><month>09</month><year>2014</year></pub-date><pub-date pub-type="collection"><year>2014</year></pub-date><volume>3</volume><elocation-id>e03430</elocation-id><history><date date-type="received"><day>21</day><month>05</month><year>2014</year></date><date date-type="accepted"><day>23</day><month>09</month><year>2014</year></date></history><permissions><copyright-statement>© 2014, Hopf et al</copyright-statement><copyright-year>2014</copyright-year><copyright-holder>Hopf et al</copyright-holder><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This article is distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use and redistribution provided that the original author and source are credited.</license-p></license></permissions><self-uri content-type="pdf" xlink:href="elife03430.pdf"/><abstract><object-id pub-id-type="doi">10.7554/eLife.03430.001</object-id><p>Protein–protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions, and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source of information about protein interactions is the evolutionary sequence record. Building on earlier work, we show that analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in space with sufficient accuracy to determine the three-dimensional structure of the protein complexes. We evaluate prediction performance in blinded tests on 76 complexes of known 3D structure, predict protein–protein contacts in 32 complexes of unknown structure, and demonstrate how evolutionary couplings can be used to distinguish between interacting and non-interacting protein pairs in a large complex. With the current growth of sequences, we expect that the method can be generalized to genome-wide elucidation of protein–protein interaction networks and used for interaction predictions at residue resolution.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.001">http://dx.doi.org/10.7554/eLife.03430.001</ext-link></p></abstract><abstract abstract-type="executive-summary"><object-id pub-id-type="doi">10.7554/eLife.03430.002</object-id><title>eLife digest</title><p>DNA is often referred to as the ‘blueprint of life’, as this molecule contains the instructions that are required to build a living organism from a single cell. But these instructions largely play out through the proteins that DNA encodes; and most proteins do not work alone. Instead they come together in different combinations, or complexes, and a single protein may participate in many complexes with different activities.</p><p>Proteins are so small that it is difficult to get clear information about what they look like. Visualizing protein complexes is even harder. Most protein–protein interactions remain poorly understood, even in the best-studied organisms such as humans, yeast, and bacteria.</p><p>Proteins are made from smaller molecules, called amino acids, strung together one after the other. The order in which different amino acids are arranged in a protein determines the protein’s shape and ultimately its function. Like DNA, protein sequences can change over time. Sometimes, the sequence of one protein changes in a way that prevents it binding to another protein. If these two proteins must work together for an organism to survive, the second protein will often develop a compensating change that allows the protein–protein complex to reform.</p><p>Identifying pairs of changes in the sequences of pairs of proteins suggests that the two proteins interact and gives some information about how the proteins fit together. Different species can have copies of the same proteins that have slightly different sequences. Since the DNA sequences from many different organisms are already known, there are now many opportunities to find sites in pairs of proteins that have evolved together, or co-evolved, over time.</p><p>To find sites that seem to have co-evolved, Hopf et al. used a computer program based on an approach from statistical physics to look at pairs of proteins that were already known to form complexes. Co-evolving sites were found in over 300 pairs of proteins; including 76 where the structure of the complex was already known. When sites that were predicted to be co-evolving were then mapped to these known complex structures, the co-evolving sites were remarkably close to the true protein–protein contacts. This indicates that the information from the co-evolved sequences is sufficient to show how two proteins fit together.</p><p>Hopf et al. then turned their attention to 82 pairs of proteins that were thought to interact, but where a structure was unavailable. For 32 of these pairs, structures of the entire complex could be predicted, showing how the two proteins might interact. Furthermore, when other researchers subsequently worked out the structure of one of these complexes, the prediction was a good match to the solved complex structure.</p><p>The machinery of life is largely made up of proteins, which must interact in ever-changing but precise ways. The new methods developed by Hopf et al. provide a new way to discover and investigate the details of these interactions.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.002">http://dx.doi.org/10.7554/eLife.03430.002</ext-link></p></abstract><kwd-group kwd-group-type="author-keywords"><title>Author keywords</title><kwd>co-evolution</kwd><kwd>protein</kwd><kwd>interactions</kwd></kwd-group><kwd-group kwd-group-type="research-organism"><title>Research organism</title><kwd><italic>E. coli</italic></kwd></kwd-group><funding-group><award-group id="par-1"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/100000057</institution-id><institution>National Institute of General Medical Sciences</institution></institution-wrap></funding-source><award-id>R01 GM106303</award-id><principal-award-recipient><name><surname>Hopf</surname><given-names>Thomas A</given-names></name><name><surname>Marks</surname><given-names>Debora S</given-names></name><name><surname>Sander</surname><given-names>Chris</given-names></name></principal-award-recipient></award-group><award-group id="par-2"><funding-source><institution-wrap><institution-id institution-id-type="FundRef">http://dx.doi.org/10.13039/501100000592</institution-id><institution>Fulbright Commission</institution></institution-wrap></funding-source><principal-award-recipient><name><surname>Schärfe</surname><given-names>Charlotta P I</given-names></name></principal-award-recipient></award-group><funding-statement>The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.</funding-statement></funding-group><custom-meta-group><custom-meta><meta-name>elife-xml-version</meta-name><meta-value>2</meta-value></custom-meta><custom-meta specific-use="meta-only"><meta-name>Author impact statement</meta-name><meta-value>Interactions in protein complexes can be predicted from evolutionary information from genomic sequences.</meta-value></custom-meta></custom-meta-group></article-meta></front><body><sec id="s1" sec-type="intro"><title>Introduction</title><p>A large part of biological research is concerned with the identity, dynamics, and specificity of protein interactions. There have been impressive advances in the three-dimensional (3D) structure determination of protein complexes which has been significantly extended by homology-inferred 3D models (<xref ref-type="bibr" rid="bib43">Mosca et al., 2012</xref>; <xref ref-type="bibr" rid="bib65">Webb et al., 2014</xref>) (<xref ref-type="bibr" rid="bib23">Hart et al., 2006</xref>; <xref ref-type="bibr" rid="bib67">Zhang et al., 2012</xref>). However, there is still little, or no, 3D information for ∼80% of the currently known protein interactions in bacteria, yeast, or human, amounting to at least ∼30,000/∼6000 incompletely characterized interactions in human and <italic>Escherichia coli,</italic> respectively (<xref ref-type="bibr" rid="bib43">Mosca et al., 2012</xref>; <xref ref-type="bibr" rid="bib51">Rajagopala et al., 2014</xref>). With the rapid rise in our knowledge of genetic variation at the sequence level, there is an increased interest in linking sequence changes to changes in molecular interactions, but current experimental methods cannot match the increase in the demand for residue-level information of these interactions. One way to address the knowledge gap of protein interactions has been the use of hybrid, computational–experimental approaches that typically combine 3D structural information at varying resolutions, homology models, and other methods (<xref ref-type="bibr" rid="bib12">de Juan et al., 2013</xref>), with force field-based approaches such as RosettaDock, residue cross-linking, and data-driven approaches that incorporate various sources of biological information (<xref ref-type="bibr" rid="bib32">Kortemme and Baker, 2002</xref>; <xref ref-type="bibr" rid="bib17">Dominguez et al., 2003</xref>; <xref ref-type="bibr" rid="bib33">Kortemme and Baker, 2004</xref>; <xref ref-type="bibr" rid="bib34">Kortemme et al., 2004</xref>; <xref ref-type="bibr" rid="bib60">Svensson et al., 2004</xref>; <xref ref-type="bibr" rid="bib10">Chaudhury et al., 2011</xref>; <xref ref-type="bibr" rid="bib56">Schneidman-Duhovny et al., 2012</xref>; <xref ref-type="bibr" rid="bib63">Velazquez-Muriel et al., 2012</xref>; <xref ref-type="bibr" rid="bib31">Karaca and Bonvin, 2013</xref>; <xref ref-type="bibr" rid="bib54">Rodrigues et al., 2013</xref>; <xref ref-type="bibr" rid="bib65">Webb et al., 2014</xref>). However, most of these approaches depend on the availability of prior knowledge and many biologically relevant systems remain out of reach, as additional experimental information is sparse (e.g., membrane proteins, transient interactions, and large complexes). One promising computational approach is to use evolutionary analysis of amino acid co-variation to identify close residue contacts across protein interactions, which was first used 20 years ago (<xref ref-type="bibr" rid="bib22">Gobel et al., 1994</xref>; <xref ref-type="bibr" rid="bib47">Pazos and Valencia, 2001</xref>), and subsequently used also to identify protein interactions (<xref ref-type="bibr" rid="bib49">Pazos et al., 1997</xref>; <xref ref-type="bibr" rid="bib48">Pazos and Valencia, 2002</xref>). Others have used some evolutionary information to improve a machine learning approach to developing docking potentials (<xref ref-type="bibr" rid="bib19">Faure et al., 2012</xref>; <xref ref-type="bibr" rid="bib2">Andreani et al., 2013</xref>; <xref ref-type="bibr" rid="bib1">Andreani and Guerois, 2014</xref>). These previous approaches relied on a local model of co-evolution that is less likely to disentangle indirect and therefore incorrect correlations from the direct co-evolution, as has been described in work on residue–residue interactions in single proteins (<xref ref-type="bibr" rid="bib40">Marks et al., 2012</xref>). More recently, reports using a global model have been successful in identifying residue interactions from evolutionary co-variation, for instance between histidine kinases and response regulators (<xref ref-type="bibr" rid="bib9">Burger & van Nimwegen, 2008</xref>; <xref ref-type="bibr" rid="bib59">Skerker et al., 2008</xref>; <xref ref-type="bibr" rid="bib66">Weigt et al., 2009</xref>), and this approach has only recently been generalized and used to predict contacts between proteins in complexes of unknown structure, in an independent effort parallel to this work (<xref ref-type="bibr" rid="bib45">Ovchinnikov et al., 2014</xref>). In principle, just a small number of key residue–residue contacts across a protein interface would allow computation of 3D models and provide a powerful, orthogonal approach to experiments.</p><p>Since the recent demonstration of the use of evolutionary couplings (ECs) between residues to determine the 3D structure of individual proteins (<xref ref-type="bibr" rid="bib39">Marks et al., 2011</xref>; <xref ref-type="bibr" rid="bib42">Morcos et al., 2011</xref>; <xref ref-type="bibr" rid="bib3">Aurell and Ekeberg, 2012</xref>; <xref ref-type="bibr" rid="bib28">Jones et al., 2012</xref>; <xref ref-type="bibr" rid="bib30">Kamisetty et al., 2013</xref>), including integral membrane proteins (<xref ref-type="bibr" rid="bib24">Hopf et al., 2012</xref>; <xref ref-type="bibr" rid="bib44">Nugent and Jones, 2012</xref>), we reason that an evolutionary statistical approach such as EVcouplings (<xref ref-type="bibr" rid="bib39">Marks et al., 2011</xref>) could be used to determine co-evolved residues <italic>between</italic> proteins. To assess this hypothesis, we built an evaluation set based on all known binary protein interactions in <italic>E. coli</italic> that have 3D structures of the complex as recently summarized (<xref ref-type="bibr" rid="bib51">Rajagopala et al., 2014</xref>). We develop a score for every predicted inter-protein residue pair based on the overall inter-protein EC score distributions resulting in accurate predictions for the majority of top ranked <italic>inter</italic>-protein EC pairs (inter-ECs) and sufficient to calculate accurate 3D models of the complexes in the docked subset (<xref ref-type="fig" rid="fig1">Figure 1A</xref>). This approach was then used to predict evolutionary couplings for 32 complexes of unknown 3D structures that have a sufficient number of sequences. Predictions include the structurally unsolved interactions between the a-, b-, and c-subunits of ATP synthase, which are supported by previously published experimental results.<fig-group><fig id="fig1" position="float"><object-id pub-id-type="doi">10.7554/eLife.03430.003</object-id><label>Figure 1.</label><caption><title>Co-evolution of residues across protein complexes from the evolutionary sequence record.</title><p>(<bold>A</bold>) Evolutionary pressure to maintain protein–protein interactions leads to the co-evolution of residues between interacting proteins in a complex. By analyzing patterns of amino acid co-variation in an alignment of putatively interacting homologous proteins (left), evolutionary couplings between co-evolving inter-protein residue pairs can be identified (middle). By defining distance restraints on these pairs, the 3D structure of the protein complex can be inferred using docking software (right). (<bold>B</bold>) Distribution of <italic>E. coli</italic> protein complexes of known and unknown 3D structure where both subunits are close on the bacterial genome (left), allowing sequence pair matching by genomic distance. For a subset of these complexes, sufficient sequence information is available for evolutionary couplings analysis (dark blue bars). As more genomic information is created through on-going sequencing efforts, larger fractions of the <italic>E. coli</italic> interactome become accessible for EVcomplex (right). A detailed version of the workflow used to calculate all <italic>E. coli</italic> complexes currently for which there is currently enough sequence information is shown in <xref ref-type="fig" rid="fig1s1">Figure1—figure supplement 1</xref>.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.003">http://dx.doi.org/10.7554/eLife.03430.003</ext-link></p></caption><graphic xlink:href="elife03430f001"/></fig><fig id="fig1s1" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.03430.004</object-id><label>Figure 1—figure supplement 1.</label><caption><title>Details of the EVcomplex Pipeline.</title><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.004">http://dx.doi.org/10.7554/eLife.03430.004</ext-link></p></caption><graphic xlink:href="elife03430fs001"/></fig></fig-group></p></sec><sec id="s2" sec-type="results"><title>Results</title><p>We first investigated whether co-evolving residues between proteins are close in three dimensions by assessing blinded predictions of residue co-evolution against experimentally determined 3D complex structures. We follow this evaluation by then predicting co-evolved residue pairs of interacting proteins that have no known complex structure.</p><sec id="s2-1"><title>Extension of the evolutionary couplings method to protein complexes</title><p>To compute co-evolution across proteins, individual protein sequences must be paired up with each other that are presumed to interact, or being tested to see if they interact. Without this condition, proteins could be paired together that do not in fact interact with each other and therefore detection of co-evolution would be compromised. Given that the evolutionary couplings method depends on large numbers of diverse sequences (<xref ref-type="bibr" rid="bib24">Hopf et al., 2012</xref>), some assumption must be made about which proteins interact with each other in homologous sequences in other species. Since it is challenging to know a priori whether particular interactions are conserved across many millions of years in thousands of different organisms, we use proximity of the two interacting partners on the genome as a proxy for this, with the goal of reducing incorrect pairings.</p><p>To assemble the broadest possible data sets to test the approach and make predictions, we take all known interacting proteins assembled in a published data set that contains ∼3500 high-confidence protein interactions in <italic>E. coli</italic> (<xref ref-type="bibr" rid="bib51">Rajagopala et al., 2014</xref>). After removing redundancy and requiring close genome distance between the pairs of proteins this results in 326 interactions, see ‘Materials and methods’ (<xref ref-type="fig" rid="fig1">Figure 1B</xref>, <xref ref-type="fig" rid="fig1s1">Figure 1—figure supplement 1</xref>, <xref ref-type="supplementary-material" rid="SD1-data SD2-data">Supplementary file 1 and 2</xref>),</p><p>The paired sequences are concatenated and statistical co-evolution analysis is performed using EVcouplings (<xref ref-type="bibr" rid="bib39">Marks et al., 2011</xref>; <xref ref-type="bibr" rid="bib42">Morcos et al., 2011</xref>; <xref ref-type="bibr" rid="bib3">Aurell and Ekeberg, 2012</xref>), that applies a pseudolikelihood maximization (PLM) approximation to determine the interaction parameters in the underlying maximum entropy probability model (<xref ref-type="bibr" rid="bib5">Balakrishnan et al., 2011</xref>; <xref ref-type="bibr" rid="bib18">Ekeberg et al., 2013</xref>; <xref ref-type="bibr" rid="bib30">Kamisetty et al., 2013</xref>), simultaneously generating both intra- and inter-EC scores for all pairs of residues within and across the protein pairs (<xref ref-type="fig" rid="fig1">Figure 1A</xref>). Evolutionary coupling calculations in previous work have indicated that this global probability model approach requires a minimum number of sequences in the alignment with at least 1 non-redundant sequence per residue (<xref ref-type="bibr" rid="bib39">Marks et al., 2011</xref>; <xref ref-type="bibr" rid="bib42">Morcos et al., 2011</xref>; <xref ref-type="bibr" rid="bib24">Hopf et al., 2012</xref>; <xref ref-type="bibr" rid="bib28">Jones et al., 2012</xref>; <xref ref-type="bibr" rid="bib30">Kamisetty et al., 2013</xref>). Our current approach allows complexes with fewer available sequences to be assessed (minimum at 0.3 non-redundant sequences per residue) by using a new quality assessment score to assess the likelihood of the predicted contacts to be correct. The EVcomplex score is based on the knowledge that most pairs of residues are not coupled and true pair couplings are outliers in the high-scoring tail of the distribution (See ‘Materials and methods’, <xref ref-type="fig" rid="fig2">Figure 2A,B</xref>, <xref ref-type="fig" rid="fig2s1 fig2s2">Figure 2—figure supplement 1 and 2</xref>). The score can intuitively be understood as the distance from the noisy background of non-significant pair scores, normalized by the number of non-redundant sequences and the length of the protein (‘Materials and methods’, <xref ref-type="disp-formula" rid="equ1">equations 1</xref> and <xref ref-type="disp-formula" rid="equ2">2</xref>). If the number of sequences per residue is not controlled for, there is a large bias in the results, overestimating performance with low numbers of sequences (<xref ref-type="fig" rid="fig2">Figure 2B,C</xref>). The precise functional form of the correction for low numbers of sequences was chosen non-blindly after observing the dependencies in the test set.<fig-group><fig id="fig2" position="float"><object-id pub-id-type="doi">10.7554/eLife.03430.005</object-id><label>Figure 2.</label><caption><title>Evolutionary couplings capture interacting residues in protein complexes.</title><p>(<bold>A</bold>) Inter- and Intra-EC pairs with high coupling scores largely correspond to proximal pairs in 3D, but only if they lie above the background level of the coupling score distribution. To estimate this background noise a symmetric range around 0 is considered with the width being defined by the minimum inter-EC score. For the protein complexes in the evaluation set, this distribution is compared to the distance in the known 3D structure of the complex that is shown here for the methionine transporter complex, MetNI. (Plots for all complexes in the evaluation set are shown in <xref ref-type="fig" rid="fig2s1 fig2s2">Figure 2—figure supplement 1 and 2</xref>.) (<bold>B</bold>) A larger distance from the background noise (ratio of EC score over background noise line) gives more accurate contacts. Additionally, the higher the number of sequences in the alignment the more reliable the inferred coupling pairs are which then reduces the required distance from noise (different shades of blue). Residue pairs with an 8 Å minimum atom distance between the residues are defined as true positive contacts, and precision = TP/(TP + FP). The plot is limited to range (0,3) which excludes the histidine kinase—response regulator complex (HK–RR)—a single outlier with extremely high number of sequences. (<bold>C</bold>) To allow the comparison across protein complexes and to estimate the average inter-EC precision for a given score threshold independent of sequence numbers, the raw couplings score is normalized for the number of sequences in the alignment, resulting in the EVcomplex score. In this work, inter-ECs with an EVcomplex score ≥0.8 are used. Note: the shown plot is cut off at a score of 2 in order to zoom in on the phase change region and the high sequence coverage outlier HK-RR is excluded. (<bold>D</bold>) For complexes in the benchmark set, inter-EC pairs with EVcomplex score ≥0.8 give predictions of interacting residue pairs between the complex subunits to varying accuracy (8 Å TP distance cutoff). All predicted interacting residues for complexes in the benchmark set that had at least one inter-EC above 0.8 are shown as contact maps in <xref ref-type="fig" rid="fig2s3 fig2s4 fig2s5 fig2s6 fig2s7 fig2s8">Figure 2—figure supplement 3–8</xref>.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.005">http://dx.doi.org/10.7554/eLife.03430.005</ext-link></p></caption><graphic xlink:href="elife03430f002"/></fig><fig id="fig2s1" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.03430.006</object-id><label>Figure 2—figure supplement 1.</label><caption><title>Distribution and accuracy of raw EC scores for all complexes in evaluation set.</title><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.006">http://dx.doi.org/10.7554/eLife.03430.006</ext-link></p></caption><graphic xlink:href="elife03430fs002"/></fig><fig id="fig2s2" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.03430.007</object-id><label>Figure 2—figure supplement 2.</label><caption><title>Distribution and accuracy of raw EC scores for all complexes in evaluation set (2).</title><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.007">http://dx.doi.org/10.7554/eLife.03430.007</ext-link></p></caption><graphic xlink:href="elife03430fs003"/></fig><fig id="fig2s3" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.03430.008</object-id><label>Figure 2—figure supplement 3.</label><caption><title>Contact maps of all complexes with solved 3D structure with inter-ECs above EVcomplex score of 0.8.</title><p>Predicted coevolving residue pairs with an EVcomplex score ≥0.8 and all inter-ECs up to the rank of the last include inter-EC are visualized in complex contact maps (red dots: inter-ECs, green and blue dots: intra-ECs for monomer 1 and 2, respectively). Top left and bottom right quadrants: intra-ECs; top right and bottom left quadrants: inter-ECs. Inter- and intra-protein crystal structure contacts at minimum atom distance cutoffs of 5/8/12 Å are shown as dark/middle/light gray dots, respectively; missing data in the crystal structure as shaded blue rectangles.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.008">http://dx.doi.org/10.7554/eLife.03430.008</ext-link></p></caption><graphic xlink:href="elife03430fs004"/></fig><fig id="fig2s4" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.03430.009</object-id><label>Figure 2—figure supplement 4.</label><caption><title>Contact maps of all complexes with solved 3D structure with inter-ECs above EVcomplex score of 0.8 (2).</title><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.009">http://dx.doi.org/10.7554/eLife.03430.009</ext-link></p></caption><graphic xlink:href="elife03430fs005"/></fig><fig id="fig2s5" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.03430.010</object-id><label>Figure 2—figure supplement 5.</label><caption><title>Contact maps of all complexes with solved 3D structure with inter-ECs above EVcomplex score of 0.8 (3).</title><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.010">http://dx.doi.org/10.7554/eLife.03430.010</ext-link></p></caption><graphic xlink:href="elife03430fs006"/></fig><fig id="fig2s6" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.03430.011</object-id><label>Figure 2—figure supplement 6.</label><caption><title>Contact maps of all complexes with solved 3D structure with inter-ECs above EVcomplex score of 0.8 (4).</title><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.011">http://dx.doi.org/10.7554/eLife.03430.011</ext-link></p></caption><graphic xlink:href="elife03430fs007"/></fig><fig id="fig2s7" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.03430.012</object-id><label>Figure 2—figure supplement 7.</label><caption><title>Contact maps of all complexes with solved 3D structure with inter-ECs above EVcomplex score of 0.8 (5).</title><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.012">http://dx.doi.org/10.7554/eLife.03430.012</ext-link></p></caption><graphic xlink:href="elife03430fs008"/></fig><fig id="fig2s8" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.03430.013</object-id><label>Figure 2—figure supplement 8.</label><caption><title>Contact maps of all complexes with solved 3D structure with inter-ECs above EVcomplex score of 0.8 (6).</title><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.013">http://dx.doi.org/10.7554/eLife.03430.013</ext-link></p></caption><graphic xlink:href="elife03430fs009"/></fig></fig-group></p></sec><sec id="s2-2"><title>Blinded prediction of known complexes</title><sec id="s2-2-1"><title>Evolutionary covariation reveals inter-protein contacts</title><p>Of the 329 interactions identified that are close on the <italic>E. coli</italic> genome, 76 have a sufficient number of alignable homologous sequences and known 3D structures either in <italic>E. coli</italic> or in other species. This set was used to test the inter-protein evolutionary coupling predictions (<xref ref-type="supplementary-material" rid="SD1-data">Supplementary file 1</xref>). The relationship between the EVcomplex score and the precision of the corresponding inter-protein ECs suggests that on average 74% (69%) of the predicted pairs with EVcomplex score greater than 0.8 will be accurate to within 10 Å (8 Å) of an experimental structure of the complex (<xref ref-type="fig" rid="fig2">Figure 2C</xref>). Most complexes have at least one inter-protein predicted contact above the selected score threshold of 0.8 (53/76 complexes). Three complexes have more than 20 predicted inter-protein residue contacts which are over 80% accurate, namely the histidine kinase and response regulator system (78 residue pairs), t-RNA synthetase (32 residue pairs), and the vitamin B importer complex (21 residue pairs), with precision over 80% (complex numbers 330, 019, 130 respectively, <xref ref-type="fig" rid="fig2">Figure 2D</xref>, <xref ref-type="fig" rid="fig2s3 fig2s4 fig2s5 fig2s6 fig2s7 fig2s8">Figure 2—figure supplements 3–8</xref>, <xref ref-type="supplementary-material" rid="SD1-data">Supplementary file 1</xref>).</p><p>We suggest that users of EVcomplex consider predicted contacts that lie below the threshold of 0.8 in the context of other biological knowledge, where available, or in comparison to other higher scoring contacts for the same complex. In this way additional true positive inter-residue contacts can be distinguished from false positives. For instance, the ethanolamine ammonia-lyase complex (complex 065) has only 3 predicted inter-protein residue pairs above the score threshold, but in fact has 5 additional correct pairs with EVcomplex scores slightly below the threshold of 0.8 which cluster with the 3 high-scoring contacts on the monomers, indicating that they are also correct.</p><p>Some of the high confidence inter-protein ECs in the test set are not close in 3D space when compared to their known 3D structures. These false positives may be a result of assumptions in the method that are not always correct. This includes (1) the assumption that the interaction between paired proteins is conserved across species and across paralogs, and (2) that truly co-evolved residues across proteins are indeed always close in 3D, which is not always the case. In addition, the complexes may also exist in alternative conformations that have not necessarily all been captured yet by crystal or NMR structures, for instance in the case of the large conformational changes of the BtuCDF complex (<xref ref-type="bibr" rid="bib25">Hvorup et al., 2007</xref>).</p></sec><sec id="s2-2-2"><title>Docking is accurate with few pairs of predicted contacts</title><p>To test whether the computed inter-protein ECs are sufficient for obtaining accurate 3D structures of the whole complex, we selected 15 diverse examples (with 5 or more inter-protein residue contacts) for docking (<xref ref-type="table" rid="tbl1">Table 1</xref>, <xref ref-type="fig" rid="fig3">Figure 3</xref>, <xref ref-type="fig" rid="fig3s1">Figure 3—figure supplement 1</xref>, <xref ref-type="supplementary-material" rid="SD3-data">Supplementary file 3</xref>) with HADDOCK (<xref ref-type="bibr" rid="bib17">Dominguez et al., 2003</xref>; <xref ref-type="bibr" rid="bib13">de Vries et al., 2007</xref>). The docking procedure is fast and generates 100 3D models of each complex using all residue pairs with EVcomplex scores above the selection threshold. We additionally dock negative controls to assess the amount of information added to the docking protocol by evolutionary couplings (500 models per run, no constraints other than center of mass, see ‘Materials and methods’). The best models for all 15 complexes docked with evolutionary couplings have interface RMSDs under 6 Å, 12/15 have the best scoring model under 4 Å and the top ranked models for 11/15 are under 5 Å backbone interface RMSD compared to a crystal or NMR structure interface. Over 70% of the generated models are close to the experimental structures of the complexes (<4 Å backbone iRMSD), compared to less than 0.5% in the controls (and these were not high–ranked) (<xref ref-type="fig" rid="fig3s1">Figure 3—figure supplement 1</xref>, <xref ref-type="supplementary-material" rid="SD3-data">Supplementary file 3</xref>, ‘Supplementary data’). Not surprisingly complexes that have the largest numbers of true positive predicted contacts perform the best when docking. For example, the ribosomal proteins RS3 and RS14 have 11 true positive inter-protein ECs and result in a top ranked model only 1.1 Å iRMSD from the reference structure. More surprisingly, other complexes with a lower proportion of true positive inter-protein contacts, such as Ubiquinol oxidase (6 out of 11) or the epsilon and gamma subunits of ATP synthase (8 out of 15) also produced accurate predicted complexes, with an iRMSD of 1.8 and 1.4 Å respectively. The docking experiments therefore demonstrate that inter-protein ECs, even in the presence of incorrect predictions, can be sufficient to give accurate 3D models of protein complexes, but more work will be needed to quantify the likelihood of successful docking from the predicted contacts.<table-wrap id="tbl1" position="float"><object-id pub-id-type="doi">10.7554/eLife.03430.014</object-id><label>Table 1.</label><caption><p>EVcomplex predictions and docking results for 15 protein complexes</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.014">http://dx.doi.org/10.7554/eLife.03430.014</ext-link></p></caption><table frame="hsides" rules="groups"><thead><tr><th/><th/><th colspan="3">EVcomplex contacts</th><th colspan="2">Docking quality (iRMSD)</th></tr><tr><th>Complex name</th><th>Subunits</th><th>Seqs<xref ref-type="table-fn" rid="tblfn1">†</xref></th><th>ECs<xref ref-type="table-fn" rid="tblfn2">‡</xref></th><th>TP rate<xref ref-type="table-fn" rid="tblfn3">§</xref></th><th>Top ranked model<xref ref-type="table-fn" rid="tblfn4">#</xref></th><th>Best model<xref ref-type="table-fn" rid="tblfn5">¶</xref></th></tr></thead><tbody><tr><td>Carbamoyl-phosphate synthase</td><td>CarB:CarA</td><td>2.3</td><td>17</td><td>0.88</td><td>1.9</td><td>1.9</td></tr><tr><td>Aminomethyltransferase/Glycine cleavage system H protein</td><td>GcsH:GcsT</td><td>2.9</td><td>5</td><td>0.2</td><td>5.4</td><td>5.4</td></tr><tr><td>Histidine kinase/response regulator</td><td>KdpD:CheY (T. maritima)</td><td>95.4</td><td>78</td><td>0.72</td><td>2.1</td><td>2.0</td></tr><tr><td>Ubiquinol oxidase</td><td>CyoB:CyoA</td><td>1.0</td><td>11</td><td>0.55</td><td>1.8</td><td>1.2</td></tr><tr><td>Outer membrane usher protein/Chaperone protein</td><td>FimD:FimC</td><td>3.6</td><td>6</td><td>0.83</td><td>3.2</td><td>3.0</td></tr><tr><td>Molybdopterin synthase</td><td>MoaD:MoaE</td><td>3.6</td><td>8</td><td>1.0</td><td>4.4</td><td>4.1</td></tr><tr><td>Methionine transporter complex</td><td>MetN:MetI</td><td>1.9</td><td>14</td><td>0.86</td><td>1.5</td><td>1.2</td></tr><tr><td>Dihydroxyacetone kinase</td><td>DhaL:DhaK</td><td>1.4</td><td>12</td><td>0.42</td><td>6.7</td><td>2.4</td></tr><tr><td>Vitamin B12 uptake system</td><td>BtuC:BtuF</td><td>3.2</td><td>5</td><td>0.6</td><td>2.8</td><td>2.8</td></tr><tr><td>Vitamin B12 uptake system</td><td>BtuC:BtuD</td><td>9.8</td><td>21</td><td>0.88</td><td>1.1</td><td>0.9</td></tr><tr><td>ATP synthase γ and ε subunits</td><td>AtpE:AtpG</td><td>2.9</td><td>15</td><td>0.53</td><td>1.4</td><td>1.4</td></tr><tr><td>IIA-IIB complex of the N,N'-diacetylchitobiose (Chb) transporter</td><td>PtqA:PtqB</td><td>3.1</td><td>5</td><td>0.2</td><td>7.2</td><td>5.5</td></tr><tr><td>30 S Ribosomal proteins</td><td>RS3:RS14</td><td>1.4</td><td>11</td><td>0.91</td><td>1.1</td><td>1.1</td></tr><tr><td>Succinatequinone oxido-reductase flavoprotein/iron-sulfur subunits</td><td>SdhB:SdhA</td><td>3.0</td><td>8</td><td>0.62</td><td>1.4</td><td>1.4</td></tr><tr><td>30 S Ribosomal proteins</td><td>RS10:RS14</td><td>1.2</td><td>6</td><td>1.0</td><td>5.3</td><td>2.5</td></tr></tbody></table><table-wrap-foot><fn id="tblfn1"><label>†</label><p>Number of non-redundant sequences in concatenated alignment normalized by alignment length.</p></fn><fn id="tblfn2"><label>‡</label><p>Inter-ECs with EVcomplex score ≥0.8.</p></fn><fn id="tblfn3"><label>§</label><p>True Positive rate for inter-ECs above score threshold.</p></fn><fn id="tblfn4"><label>#</label><p>iRMSD positional deviation of model from known structure, for docked model with best HADDOCK score.</p></fn><fn id="tblfn5"><label>¶</label><p>Lowest iRMSD observed across all models.</p></fn></table-wrap-foot></table-wrap><fig-group><fig id="fig3" position="float"><object-id pub-id-type="doi">10.7554/eLife.03430.015</object-id><label>Figure 3.</label><caption><title>Blinded prediction of evolutionary couplings between complex subunits with known 3D structure.</title><p>Inter-ECs with EVcomplex score ≥0.8 on a selection of benchmark complexes (monomer subunits in green and blue, inter-ECs in red, pairs closer than 8 Å by solid red lines, dashed otherwise). The predicted inter-ECs for these ten complexes were then used to create full 3D models of the complex using protein–protein docking. For the fifteen complexes for which 3D structures were predicted using docking, energy funnels are shown in <xref ref-type="fig" rid="fig3s1">Figure 3—figure supplement 1</xref>.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.015">http://dx.doi.org/10.7554/eLife.03430.015</ext-link></p></caption><graphic xlink:href="elife03430f003"/></fig><fig id="fig3s1" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.03430.016</object-id><label>Figure 3—figure supplement 1.</label><caption><title>Comparison of Interface RMSD to HADDOCK score.</title><p>The HADDOCK scores of docked models are plotted against their iRMSDs to the bound complex crystal. Gray data points correspond to models created without any ECs as unambiguous restraints whereas blue dots correspond to model created using all inter-couplings with EVcomplex score ≥0.8. HADDOCK score outliers with scores >100 are not shown, and any model with an iRMSD >35 Å is displayed as iRMSD = 35 Å for visualization purposes.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.016">http://dx.doi.org/10.7554/eLife.03430.016</ext-link></p></caption><graphic xlink:href="elife03430fs010"/></fig></fig-group></p></sec><sec id="s2-2-3"><title>Conserved residue networks provide evidence of functional constraints</title><p>The top 10 inter-EC pairs between MetI and MetN are accurate to within 8 Å in the MetNI complex (PDB: 3tui [<xref ref-type="bibr" rid="bib27">Johnson et al., 2012</xref>]), resulting in an average 1.4 Å iRMSD from the crystal structure for all 100 computed 3D models (<xref ref-type="table" rid="tbl1">Table 1</xref>, <xref ref-type="supplementary-material" rid="SD3-data">Supplementary file 3</xref> and ‘Supplementary data’). The top 3 inter-EC residue pairs (K136-E108, A128-L105, and E74-R124, MetI-MetN respectively) constitute a residue network coupling the ATP-binding pocket of MetN to the membrane transporter MetI. This network calculated from the sequence alignment corresponds to residues identified experimentally that couple ATP hydrolysis to the open and closed conformations of the MetI dimer (<xref ref-type="bibr" rid="bib27">Johnson et al., 2012</xref>) (<xref ref-type="fig" rid="fig4">Figure 4A</xref>). The vitamin B12 transporter (BtuC) belongs to a different structural class of ABC transporters, but also uses ATP hydrolysis via an interacting ATPase (BtuD). The top 5 inter-ECs co-locate the L-loop of BtuC close to the Q-loop ATP-binding domain of the ATPase, hence coupling the transporter with the ATP hydrolysis state in an analogous way to MetI-MetN. The identification of these coupled residues across the different subunits suggests that EVcomplex identifies not only residues close in space, but also particular pairs that are constrained by the transporter function of these complexes (<xref ref-type="bibr" rid="bib29">Kadaba et al., 2008</xref>; <xref ref-type="bibr" rid="bib27">Johnson et al., 2012</xref>).<fig id="fig4" position="float"><object-id pub-id-type="doi">10.7554/eLife.03430.017</object-id><label>Figure 4.</label><caption><title>Evolutionary couplings give accurate 3D structures of complexes.</title><p>EVcomplex predictions and comparison to crystal structure for (<bold>A</bold>) the methionine-importing transmembrane transporter heterocomplex MetNI from <italic>E. coli</italic> (PDB: 3tui) and (<bold>B</bold>) the gamma/epsilon subunit interaction of <italic>E. coli</italic> ATP synthase (PDB: 1fs0). Left panels: complex contact map comparing predicted inter-ECs with EVcomplex score ≥0.8 (red dots, upper right quadrant) and intra-ECs (up to the last chosen inter-EC rank; green and blue dots, top left and lower right triangles) to close pairs in the complex crystal (dark/mid/light gray points for minimum atom distance cutoffs of 5/8/12 Å for inter-subunit contacts and dark/mid gray for 5/8 Å within the subunits). Inter-ECs with an EVcomplex score ≥0.8 are also displayed on the spatially separated subunits of the complex (red lines on green and blue cartoons, couplings closer than 8 Å in solid red lines, dashed otherwise, lower left). Right panels: superimposition of the top ranked model from 3D docking (green/blue cartoon, left) onto the complex crystal structure (gray cartoon) and close-up of the interface region with highly coupled residues (green/blue spheres).</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.017">http://dx.doi.org/10.7554/eLife.03430.017</ext-link></p></caption><graphic xlink:href="elife03430f004"/></fig></p><p>The ATP synthase ε and γ subunit complex provides a challenge to our approach, since the ε subunit can take different positions relative to the γ subunit, executing the auto-inhibition of the enzyme by dramatic conformational changes (<xref ref-type="bibr" rid="bib11">Cingolani and Duncan, 2011</xref>). In a real-world scenario, where we might not know this a priori, there may be conflicting constraints in the evolutionary record corresponding to the different positions of the flexible portion of ε subunit. EVcomplex accurately predicts 6 of the top 10 inter-EC pairs (within 8 Å in the crystal structure 1fs0 (<xref ref-type="bibr" rid="bib53">Rodgers and Wilce, 2000</xref>) or 3oaa (<xref ref-type="bibr" rid="bib11">Cingolani and Duncan, 2011</xref>)), with the top 2 inter-ECs εA45-γL215 and εA40-γL207 providing contact between the subunits along an inter-protein beta sheet. The location of the C-terminal helices of the ε subunit is significantly different across 3 crystal structures (PDB IDs: 1fs0 [<xref ref-type="bibr" rid="bib53">Rodgers and Wilce, 2000</xref>], 1aqt [<xref ref-type="bibr" rid="bib61">Uhlin et al., 1997</xref>], 3oaa [<xref ref-type="bibr" rid="bib11">Cingolani and Duncan, 2011</xref>]). The top ranked intra-ECs support the conformation seen in 1aqt, with the C-terminal helices packed in an antiparallel manner and tucked against the N-terminal beta barrel (<xref ref-type="fig" rid="fig4">Figure 4B</xref>, green circles) and do not contain a high ranked evolutionary trace for the extended helical contact to the γ subunit seen in 1fs0 or 3oaa (<xref ref-type="fig" rid="fig4">Figure 4B</xref>, gray box). Docking with the top inter-ECs results in models with 1.4 Å backbone iRMSDs to the crystal structure for the interface between the N-terminal domain of the ε subunit and the γ subunit (<xref ref-type="table" rid="tbl1">Table 1</xref>, <xref ref-type="supplementary-material" rid="SD3-data">Supplementary file 3</xref>). εD82 and γR222 connect the ε-subunit via a network of 3 high-scoring intra-ECs between the N- and C-terminal helices to the core of the F1 ATP synthase. In summary, these examples suggest that inter-protein evolutionary couplings can provide residue relationships across the proteins that could aid identification of functional coupling pathways, in addition to obtaining 3D models of the complex.</p></sec></sec><sec id="s2-3"><title>De novo prediction of unknown complexes</title><sec id="s2-3-1"><title>Prediction of interactions for 32 protein pairs with high-scoring evolutionary couplings</title><p>A total of 82 protein complexes with unknown 3D structure of the interaction that satisfy the conditions for the current approach, i.e., have sufficient sequences and are close in all genomes, were predicted using EVcomplex (all residue–residue <italic>inter</italic>-protein evolutionary couplings scores are available in ‘Supplementary data’). 32 of these have high EVcomplex scores with at least one predicted contact (<xref ref-type="fig" rid="fig5">Figure 5</xref>, <xref ref-type="fig" rid="fig5s1 fig5s2">Figure 5—figure supplement 1 and 2</xref>, and <xref ref-type="supplementary-material" rid="SD4-data">Supplementary file 4</xref>). Analysis of the inter-EC predictions for known 3D complex structures shows that protein pairs with more high-scoring ECs (EVcomplex score ≥0.8) have a higher proportion of true positives (<xref ref-type="fig" rid="fig2">Figure 2D</xref>). Hence, the protein complexes in the set of unknown structures with more high-scoring inter-ECs are most likely to have predicted ECs that indicate residue pairs close in 3D (column Q, <xref ref-type="supplementary-material" rid="SD2-data">Supplementary file 2</xref>, the exact pairs can be found in <xref ref-type="supplementary-material" rid="SD4-data">Supplementary file 4</xref>). Three examples of predictions with multiple high-scoring inter-ECs include MetQ-MetI, UmuD-UmuC, and DinJ–YafQ. The top 15 inter-ECs between MetQ and MetI are from one interface of MetQ to the MetI periplasmic loops, or the periplasmic end of the helices, consistent with the known binding of MetQ to MetI in the periplasm.<fig-group><fig id="fig5" position="float"><object-id pub-id-type="doi">10.7554/eLife.03430.018</object-id><label>Figure 5.</label><caption><title>Evolutionary couplings in complexes of unknown 3D structure.</title><p>Inter-ECs for five de novo prediction candidates without <italic>E. coli</italic> or interaction homolog complex 3D structure (Subunits: blue/green cartoons; inter-ECs with EVcomplex score ≥0.8: red lines). For complex subunits which homomultimerize (light/dark green cartoon), inter-ECs are placed arbitrarily on either of the monomers to enable the identification of multiple interaction sites. Contact maps for all complexes with unsolved structures are provided in <xref ref-type="fig" rid="fig5s1 fig5s2">Figure 5—figure supplement 1 and 2</xref>. Left to right: (1) the membrane subunit of methionine-importing transporter heterocomplex MetI (PDB: 3tui) together with its periplasmic binding protein MetQ (Swissmodel: P28635); (2) the large and small subunits of acetolactate synthase IlvB (Swissmodel: P08142) and IlvN (PDB: 2lvw); (3) panthotenate synthase PanC (PDB: 1iho) together with ketopantoate hydroxymethyltransferase PanB (PDB: 1m3v); (4) subunits a and b of ATP synthase (model for a subunit a predict with EVfold-membrane, PDB: 1b9u for b subunit), for detailed information see <xref ref-type="fig" rid="fig6">Figure 6</xref>; and (5) the complex of UmuC (model created with EVfold) with one possible conformation of UmuD (PDB: 1i4v) involved in DNA repair and SOS mutagenesis. For alternative UmuD conformation, see <xref ref-type="fig" rid="fig5s3">Figure 5—figure supplement 3</xref>.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.018">http://dx.doi.org/10.7554/eLife.03430.018</ext-link></p></caption><graphic xlink:href="elife03430f005"/></fig><fig id="fig5s1" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.03430.019</object-id><label>Figure 5—figure supplement 1.</label><caption><title>Contact maps of all complexes without solved 3D structure with at least one inter-ECs above EVcomplex score of 0.8.</title><p>Inter-ECs are shown as red dots in the top right and bottom left quadrant while intra-ECs of the two monomers are shown in green and blue in the top left and bottom right quadrant, respectively.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.019">http://dx.doi.org/10.7554/eLife.03430.019</ext-link></p></caption><graphic xlink:href="elife03430fs011"/></fig><fig id="fig5s2" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.03430.020</object-id><label>Figure 5—figure supplement 2.</label><caption><title>Contact maps of all complexes without solved 3D structure with at least one inter-ECs above EVcomplex score of 0.8 (2).</title><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.020">http://dx.doi.org/10.7554/eLife.03430.020</ext-link></p></caption><graphic xlink:href="elife03430fs012"/></fig><fig id="fig5s3" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.03430.021</object-id><label>Figure 5—figure supplement 3.</label><caption><title>Details of the predicted UmuCD interaction residues.</title><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.021">http://dx.doi.org/10.7554/eLife.03430.021</ext-link></p></caption><graphic xlink:href="elife03430fs013"/></fig></fig-group></p><p>The UmuD and UmuC complex is induced in the stress/SOS response facilitating the cleavage of UmuD to UmuD’ (between C24 and G25) to form UmuD’<sub>2</sub> which then interacts with UmuC (DNA polymerase V) in order to copy damaged DNA (<xref ref-type="bibr" rid="bib6">Beuning et al., 2006</xref>). The truncated dimer form (UmuD’<sub>2</sub>) has at least two contrasting conformations where the N-terminal arm is placed on opposite sides of the dimer in one conformation or in close proximity in the alternative (<xref ref-type="fig" rid="fig5s3">Figure 5—figure supplement 3</xref>). For 6/7 ECs above the score threshold, residues in UmuD predicted to interface with UmuC are co-located on one face of the dimer. Two residues (Y33, I38) are located in the N-terminal arm of UmuD that, after cleavage of the 24 N-terminal amino acids, may become available for binding UmuC. Since UmuD switches functions after this cleavage and can then bind UmuC, these inter-ECs may identify the critical residues for translesion synthesis function (<xref ref-type="bibr" rid="bib6">Beuning et al., 2006</xref>). Although the ECs from this UmuD arm to UmuC involve residues in two separate domains of UmuC (S 415 and Y 74), intra-monomer evolutionary couplings predict that these residues are close in UmuC (<xref ref-type="fig" rid="fig5s3">Figure 5—figure supplement 3A</xref>, black rectangles). The relative positions of the contacting residues within each monomer therefore support the plausibility of the accuracy of the interaction interface.</p><p>Whilst this manuscript was in review, the 3D structure of the previously unsolved biofilm toxin/antitoxin DinJ–YafQ complex was published (PDB: 3mlo (<xref ref-type="bibr" rid="bib36">Liang et al., 2014</xref>)), showing the intertwining of subunits in a heterotetrameric complex. 17/19 predicted EC residue pairs are within 8 Å in this 3D structure (<xref ref-type="supplementary-material" rid="SD4-data">Supplementary file 4</xref> and ‘Supplementary data’). In general, the agreement between our de novo predicted inter-protein ECs and available experimental data serves as a measure of confidence for the predicted residue pair interactions and suggests that EVcomplex can be used to reveal 3D structural details of yet unsolved protein complexes given sufficient evolutionary information.</p></sec><sec id="s2-3-2"><title>EVcomplex predicts interacting protein pairs in a large complex</title><p>To investigate whether the EVcomplex score can also distinguish between interacting and non-interacting pairs of proteins, we use the <italic>E. coli</italic> ATP synthase complex as a test case. The ATP synthase structure is of wide biological interest (reviewed in <xref ref-type="bibr" rid="bib64">Walker, 2013</xref>) with a remarkable 3D structural arrangement, but completion of all aspects of the 3D structure has remained experimentally challenging (<xref ref-type="bibr" rid="bib4">Baker et al., 2012</xref>) (<xref ref-type="fig" rid="fig6">Figure 6A</xref>). As a demonstration exercise, we calculated evolutionary couplings for all 28 possible pair combinations of different ATP synthase subunits (centered around the <italic>E. coli</italic> ATP synthase) and transformed the ECs into EVcomplex scores for all inter-protein residue pairs (experimentally determined stoichiometry: α3β3γδεab2c10, <xref ref-type="supplementary-material" rid="SD5-data">Supplementary file 5</xref> and ‘Supplementary data’). Using the default EVcomplex score threshold of 0.8 to discriminate between interacting and non-interacting pairs of subunits, 24 of the 28 possible interactions between the subunits are correctly classified as interacting or non-interacting. The four incorrect predictions (namely: ε and c, γ and c, ε and β, b and β, for which there is some experimental evidence) are not identified as interacting using the 0.8 EVcomplex threshold. Choosing a threshold lower than 0.8 does identify 2 of these as interacting but also introduces new false positives. The ε and β interaction in the crystal structure 3oaa (<xref ref-type="bibr" rid="bib11">Cingolani and Duncan, 2011</xref>) is a special case in that it involves a highly extended conformation of the last two helices of the ε subunit that reach up into the enzyme making contacts with the β subunit. The false negative EVcomplex score for this pair could be a result of the transience of their interaction or reflect a more general problem of lack of conservation of this interaction across the aligned proteins from different species. In total 80% of the interacting residue pairs in the known 3D structure parts of the synthase complex (7 pairs of subunits) are correctly predicted (threshold: 10 Å minimum atom distance between two residues). This exercise of predicting the presence or absence of interaction between any two proteins indicates the potential of the EVcomplex method in helping to elucidate protein–protein interaction networks from evolutionary sequence co-variation and identify interacting subunits of large macromolecular complexes.<fig-group><fig id="fig6" position="float"><object-id pub-id-type="doi">10.7554/eLife.03430.022</object-id><label>Figure 6.</label><caption><title>Predicted interactions between the a-, b-, and c-subunits of ATP synthase.</title><p>(<bold>A</bold>) The a- and b- subunits of <italic>E. coli</italic> ATP synthase are known to interact, but the monomer structure of subunits a and b and the structure of their interaction in the complex are unknown. (<bold>B</bold>) EVcomplex prediction (right matrix) for ATP synthase subunit interactions compared to experimental evidence (left matrix), which is either strong (left, solid blue squares) or indicative (left, crosshatched squares). Interactions that have experimental evidence, but are not predicted at the 0.8 threshold are indicated as yellow dots. (<bold>C</bold>) Left panel: residue detail of predicted residue–residue interactions (dotted lines) between subunit a and b (residue numbers at the boundaries of transmembrane helices in gray). Right panel: proposed helix–helix interactions between ATP synthase subunits a (green), b (blue, homodimer), and the c ring (gray). The proposed structural arrangement is based on analysis of the full map of inter-subunit ECs with EVcomplex score ≥0.8 (<xref ref-type="fig" rid="fig6s1">Figure 6—figure supplement 1</xref>).</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.022">http://dx.doi.org/10.7554/eLife.03430.022</ext-link></p></caption><graphic xlink:href="elife03430f006"/></fig><fig id="fig6s1" position="float" specific-use="child-fig"><object-id pub-id-type="doi">10.7554/eLife.03430.023</object-id><label>Figure 6—figure supplement 1.</label><caption><title>Contact map of predicted ECs in the ATPsynthase a and b subunits.</title><p>Inter-ECs are shown as red dots in the top right and bottom left quadrant while intra-ECs of the two monomers are shown in green and blue in the top left and bottom right quadrant, respectively.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.023">http://dx.doi.org/10.7554/eLife.03430.023</ext-link></p></caption><graphic xlink:href="elife03430fs014"/></fig></fig-group></p></sec><sec id="s2-3-3"><title>EVcomplex predicts details of subunit interactions in ATP synthase</title><p>While much of the 3D structure of ATP synthase is known (<xref ref-type="bibr" rid="bib64">Walker, 2013</xref>), the details of interactions between the a-, b-, and c-subunits have not yet been determined by crystallography. We analyse the details in these interactions, as the EVcomplex scores between these subunits are substantial (<xref ref-type="fig" rid="fig6">Figure 6B</xref>). We are fortunately able to provide a missing piece for this analysis, the unknown structure of the membrane-integral penta-helical a-subunit, using our previously described method for de novo 3D structure prediction of alpha-helical transmembrane proteins (<xref ref-type="bibr" rid="bib24">Hopf et al., 2012</xref>). To our knowledge, there are no experimentally determined atomic resolution structures of the a-subunit of ATP synthase. A 3D model of the a-subunit is from 1999 (1c17(<xref ref-type="bibr" rid="bib52">Rastogi and Girvin, 1999</xref>)) and was computed using five helical–helical interactions that were inferred from second suppressor mutation experiments, and then imposed as distance restraints for TMH2-5, revealing a four helical bundle (with no information for TMH1). Later, cross-linking experiments (<xref ref-type="bibr" rid="bib58">Schwem and Fillingame, 2006</xref>) identified contacting residues from all pairs of helical combinations of TM2-TM5 (6 pairs), supporting the earlier 4 helical bundle topology. 7 of the 8 cross-linked pairs are either exactly the same pair (L120-I246) or adjacent to many pairs in the top L intra a-subunit evolutionary couplings (ECs).</p><p>In fact, the helix packing arrangement in the predicted structure of the a-subunit is consistent with the topology suggested on the basis of crosslinking studies (<xref ref-type="bibr" rid="bib38">Long et al., 2002</xref>; <xref ref-type="bibr" rid="bib14">DeLeon-Rangel et al., 2003</xref>; <xref ref-type="bibr" rid="bib21">Fillingame and Steed, 2014</xref>), including the lack of contacts for transmembrane helix 1 with the other 4 helices (‘Supplementary data’).</p><p>The top inter-protein EC pair between subunits a and b, aK74–bE34, coincides with experimental crosslinking evidence of the interaction of aK74 with the b-subunit and the position of E34 of the b subunit emerging from the membrane on the cytoplasmic side (<xref ref-type="bibr" rid="bib38">Long et al., 2002</xref>; <xref ref-type="bibr" rid="bib14">DeLeon-Rangel et al., 2003</xref>). Indeed, 6 of the 13 high score ECs are in the same region as the experimental crosslinks, for instance between the cytoplasmic loop between the first two helices of the a-subunit and the b-subunit helix as it emerges from the membrane bilayer (<xref ref-type="bibr" rid="bib15">DeLeon-Rangel et al., 2013</xref>), or between a239V in TM helix 5 and bL16 (<xref ref-type="fig" rid="fig6">Figure 6C</xref>, <xref ref-type="fig" rid="fig6s1">Figure 6—figure supplement 1</xref>, <xref ref-type="supplementary-material" rid="SD6-data">Supplementary file 6</xref>). Additionally, the top EC between the a- and c-subunits (aG213 – cM65) lies close to the functionally critical aR210–cD61 interaction (<xref ref-type="bibr" rid="bib16">Dmitriev et al., 1999</xref>) on the same helical faces of the respective subunits (<xref ref-type="fig" rid="fig6">Figure 6C</xref>). This prediction of missing aspects of subunit interactions may help in the design of targeted experiments to complete the understanding of the intricate molecular mechanism of the ATP synthase complex.</p></sec></sec></sec><sec id="s3" sec-type="discussion"><title>Discussion</title><p>A primary limitation of our current approach is its dependence on the availability of a large number of evolutionarily related sequences. If a protein interaction is conserved across enough sequenced genomes, using a single pair per genome can give accurate predictions of the interacting residues. However, if the protein pair is present in limited taxonomic branches, there may be insufficient sequences at any given time to make confident predictions. A solution to this could be to include multiple paralogs of the interacting proteins from each genome, but this requires correct pairing of the interaction partners, which is in general hard to ascertain. In addition, details of interactions may have diverged for paralogous pairs. Hence, in this current version of the method, we have imposed a genome distance requirement across all genomes for all homolog pairs in order to be less sensitive to these complications.</p><p>As the need to use genome proximity to pair sequences becomes less important with the increasing availability of genome sequences, there will be a dramatic increase in the number of interactions that can be inferred from evolutionary couplings, including those unique to eukaryotes. With currently available sequences (May 2014 release of the UniProt database), EVcomplex is able to provide information for about 1/10<sup>th</sup> of the known 3000 protein interactions in the <italic>E. coli</italic> genome. Once there are ∼10,000 bacterial genome sequences of sufficient diversity, one would have enough information to test each potentially interacting pair of homologs for evidence of interaction and, given sufficiently strong evolutionary couplings, infer the 3D structure of each protein–protein pair, as well as of complexes with more than two proteins. For any set of species, e.g., vertebrates or mammals, one can imagine guiding sequencing efforts to optimize species diversity to facilitate the extraction of evolutionary couplings. This can open the doors for more comprehensive and more rapid determination of approximate 3D structures of proteins and protein complexes, as well as for the elucidation in molecular detail of the most strongly evolutionarily constrained interactions, pointing to functional interactions.</p><p>Determining the three-dimensional models of complexes from the predicted contacts was successful in many of the tested instances. Using minimal computing resources and a small number of inter-EC-derived contacts, low interface positional RMSDs relative to experimental structures can be achieved. However, a significant number of proteins exist as homomultimers within larger complexes. To determine models of these complexes one must deconvolute homomultimeric inter-ECs from the intra-protein signal, which is an important technical challenge for future work.</p><p>The analysis of subunit interactions in ATP synthase in this work is a ‘proof of principle’ study showing that methods such as EVcomplex can determine which proteins interact with each other at the same time as specific residue pair couplings across the proteins (as also shown in the work by the Baker lab on ribosomal protein interactions (<xref ref-type="bibr" rid="bib45">Ovchinnikov et al., 2014</xref>)). Understanding the networks of protein interactions is of critical interest in eukaryotic systems, such as networks of protein kinases, GPCRs, or PDZ domain proteins. An understanding of the distributions of interaction specificities is of high interest to many fields. Although we do not know how well our evolutionary coupling approach will handle less obligate interactions, results on the two-component signaling system (histidine kinase/response regulator) both here and in other work (<xref ref-type="bibr" rid="bib59">Skerker et al., 2008</xref>; <xref ref-type="bibr" rid="bib66">Weigt et al., 2009</xref>) suggest optimism.</p><p>The approximately scale-free EVcomplex score is a heuristic based on the distribution of raw EC scores from the statistical model, their dependence on sequence alignment depth and the length of the concatenated sequences. The score provides a simple way of accounting for these dependencies such that a uniform threshold, say 0.8, can be used for any protein pair with the expectation of reasonably accurate predictions. Since cutoff thresholds can be useful but overly sharp, we recommend investigating predicted contacts below the threshold used in this work, especially where there is independent biological knowledge to validate the predictions.</p><p>The work presented here is in anticipation of a genome-wide exploration and, as a proof of principle, shows the accurate prediction of inter-protein contacts in many cases and their utility for the computation of 3D structures across diverse complex interfaces. As with single protein (intra-EC) predictions, evolutionarily conserved conformational flexibility and oligomerization can result in more than one set of contacts that must be de-convoluted. Can evolutionary information help to predict the details and extent for each complex? A key challenge will be the development of algorithms that can disentangle evolutionary signals caused by alternative conformations of single complexes, alternative conformations of homologous complexes, and effectively deal with false positive signals. Taken together, these issues highlight fruitful areas for future development of evolutionary coupling methods.</p><p>Despite conditions for the successful de novo calculation of co-evolved residues, the method described here may accelerate the exploration of the protein–protein interaction world and the determination of protein complexes on a genome-wide scale at residue level resolution. The use of co-evolutionary analysis in computational models to determine protein specificity and promiscuity, co-evolutionary dynamics and functional drift will open up exciting future research questions.</p></sec><sec id="s4" sec-type="materials|methods"><title>Materials and methods</title><sec id="s4-1"><title>Selection of interacting protein pairs for co-evolution calculation</title><p>The candidate set of complexes for testing and de novo prediction was derived starting from a data set of binary protein–protein interactions in <italic>E. coli</italic> including yeast two-hybrid experiments, literature-curated interactions and 3D complex structures in the PDB (<xref ref-type="bibr" rid="bib51">Rajagopala et al., 2014</xref>). Three complexes not contained in the list were added based on our analysis of other subunits in the same complex, namely BtuC/BtuF, MetI/MetQ, and the interaction between ATP synthase subunits a and b. Since our algorithm for concatenating multiple sequence pairs per species assumes the proximity of the interacting proteins on the respective genomes of each species (See below), we excluded any complex with a gene distance >20 from further analysis. The gene distance is calculated as the number of genes between the interacting partners based on an ordered list of genes in the <italic>E. coli</italic> genome obtained from the UniProt database. The resulting list of pairs (∼350) was then filtered for pseudo-homomultimeric complexes based on the identification of Pfam domains in the interacting proteins (330). All remaining complexes with a known 3D structure (as summarized in <xref ref-type="bibr" rid="bib51">Rajagopala et al., 2014</xref>) or a homologous interacting 3D structure (93) (identified by intersecting the results of HMMER searches against the PDB for both monomers) were used for evaluating the method, while complexes without known structure (236) were assigned to the de novo prediction set (<xref ref-type="fig" rid="fig1s1">Figure 1—figure supplement 1</xref>). The set with protein complexes of known 3D structure was further filtered for structures that only cover fragments (<30 amino acids) of one or both of the monomers and structures with very low resolution (>5 Å), which led to the re-assignment of Ribonucleoside-diphosphate reductase 1 (complex_002), Type I restriction-modification enzyme EcoKI (complex_012), RpoC/RpoB (complex_041), RL11/Rl7 (complex_165), the ribosome with SecY (complex_226, complex_250, and complex_255), and RS3/RS (complex_254) to the set of unknown complexes. Large proteins were run with the specific interacting domains informed by the known 3D structure, when the full sequence was too large for the number of retrieved sequences (for domain annotation see ‘Supplementary data’).</p><p>This set could serve as a benchmark set for future development efforts in the community.</p></sec><sec id="s4-2"><title>Multiple sequence alignments</title><p>Each protein from all pairs in our data set was used to generate a multiple sequence alignment (MSA) using jackhmmer (<xref ref-type="bibr" rid="bib26">Johnson et al., 2010</xref>) to search the UniProt database (<xref ref-type="bibr" rid="bib68">UniProt Consortium, 2014</xref>) with 5 iterations. To obtain alignments of consistent evolutionary depths across all the proteins, a bit score threshold of 0.5 * monomer sequence length was chosen as homolog inclusion criterion (-incdomT parameter), rather than a fixed <italic>E</italic>-value threshold which selects for different degrees of evolutionary divergence based on the length of the input sequence.</p><p>In order to calculate co-evolved residues across different proteins, the interacting pairs of sequences in each species need to be matched. Here, we assume that proteins in close proximity on the genome, e.g., on the same operon, are more likely to interact, as in the methods used previously matching histidine kinase and response regulator interacting pairs (<xref ref-type="bibr" rid="bib59">Skerker et al., 2008</xref>; <xref ref-type="bibr" rid="bib66">Weigt et al., 2009</xref>) (‘Supplementary data’). We retrieved the genomic locations of proteins in the alignments and concatenated pairs following 2 rules: (i) the CDS of each concatenated protein pair must be located on the same genomic contig (using ENA (<xref ref-type="bibr" rid="bib46">Pakseresht et al., 2014</xref>) for mapping) and (ii) each pair must be the closest to one another on the genome, when compared to all other possible pairings in the same species. The concatenated sequence pairs were filtered based on the distribution of genomic distances to exclude outlier pairs with high genomic distances of more than 10k nucleotides (‘Supplementary data’). Alignment members were clustered together and reweighted if 80% or more of their residues were identical (thus implicitly removing duplicate sequences from the alignment). <xref ref-type="supplementary-material" rid="SD1-data SD2-data">Supplementary file 1 and 2</xref> report the total number of concatenated sequences, the lengths, and the effective number of sequences remaining after down-weighting in the evaluation and de novo prediction set, respectively.</p></sec><sec id="s4-3"><title>Computation of evolutionary couplings</title><p>Inter- and intra-ECs were calculated on the alignment of concatenated sequences using a global probability model of sequence co-evolution, adapted from the method for single proteins (<xref ref-type="bibr" rid="bib39">Marks et al., 2011</xref>; <xref ref-type="bibr" rid="bib42">Morcos et al., 2011</xref>; <xref ref-type="bibr" rid="bib24">Hopf et al., 2012</xref>) using a pseudo-likelihood maximization (PLM) (<xref ref-type="bibr" rid="bib5">Balakrishnan et al., 2011</xref>; <xref ref-type="bibr" rid="bib18">Ekeberg et al., 2013</xref>) rather than mean field approximation to calculate the coupling parameters. Columns in the alignment that contain more than 80% gaps were excluded and the weight of each sequence was adjusted to represent its cluster size in the alignment thus reducing the influence of identical or near-identical sequences in the calculation. For the evaluation set, we can then compare the predicted ECs for both within and between the proteins/domains to the crystal structures of the complexes (for contact maps and all EC scores, see ‘Supplementary data’).</p></sec><sec id="s4-4"><title>Definition of a scale-free score for the assessment of interactions</title><p>In order to estimate the accuracy of the EC prediction, we evaluate the calculated inter-ECs based on the following observations: (1) most pairs of positions in an alignment are not coupled, i.e., have an EC score close to zero, and tend to be distant in the 3D structure; (2) the background distribution of EC scores between non-coupled positions is approximately symmetric around a zero mean; and (3) higher-scoring positive score outliers capture 3D proximity more accurately than lower-scoring outliers (See also <xref ref-type="fig" rid="fig2">Figure 2</xref>). The width of the (symmetric) background EC score distribution can be approximated using the absolute value of the minimal inter-EC score. The more a positive EC score exceeds the noise level of background coupling, the more likely it is to reflect true co-evolution between the coupled sites. For each inter-protein pair of sites i and j with pair coupling strength EC<sub>inter</sub>(i, j), we therefore calculate a raw reliability score ('pair coupling score ratio', <xref ref-type="fig" rid="fig2">Figure 2B</xref>) defined by<disp-formula id="equ1"><label>(1)</label><mml:math id="m1"><mml:mrow><mml:msubsup><mml:mi>Q</mml:mi><mml:mrow><mml:mtext>inter</mml:mtext></mml:mrow><mml:mrow><mml:mtext>raw</mml:mtext></mml:mrow></mml:msubsup><mml:mo>(</mml:mo><mml:mi>i</mml:mi><mml:mo>,</mml:mo><mml:mi>j</mml:mi><mml:mo>)</mml:mo><mml:mo>=</mml:mo><mml:mfrac><mml:mrow><mml:mi>E</mml:mi><mml:msub><mml:mi>C</mml:mi><mml:mrow><mml:mtext>inter</mml:mtext></mml:mrow></mml:msub><mml:mo>(</mml:mo><mml:mi>i</mml:mi><mml:mo>,</mml:mo><mml:mi>j</mml:mi><mml:mo>)</mml:mo></mml:mrow><mml:mrow><mml:mrow><mml:mo>|</mml:mo><mml:mrow><mml:munder><mml:mrow><mml:mi>min</mml:mi></mml:mrow><mml:mrow><mml:mi>i</mml:mi><mml:mo>,</mml:mo><mml:mi>j</mml:mi></mml:mrow></mml:munder><mml:mrow><mml:mo>(</mml:mo><mml:mrow><mml:mi>E</mml:mi><mml:msub><mml:mi>C</mml:mi><mml:mrow><mml:mtext>inter</mml:mtext></mml:mrow></mml:msub><mml:mrow><mml:mo>(</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>,</mml:mo><mml:mi>j</mml:mi></mml:mrow><mml:mo>)</mml:mo></mml:mrow></mml:mrow><mml:mo>)</mml:mo></mml:mrow></mml:mrow><mml:mo>|</mml:mo></mml:mrow></mml:mrow></mml:mfrac></mml:mrow></mml:math></disp-formula></p><p>Since the accuracy of evolutionary couplings critically depends both on the number and diversity of sequences in the input alignment and the size of the statistical inference problem (<xref ref-type="bibr" rid="bib39">Marks et al., 2011</xref>; <xref ref-type="bibr" rid="bib42">Morcos et al., 2011</xref>; <xref ref-type="bibr" rid="bib28">Jones et al., 2012</xref>), we incorporate a normalization factor to make the raw reliability score comparable across different protein pairs. The normalized EVcomplex score is defined as<disp-formula id="equ2"><label>(2)</label><mml:math id="m2"><mml:mrow><mml:mtext>EVcomplex</mml:mtext><mml:mo>−</mml:mo><mml:mtext>Score</mml:mtext><mml:mo>(</mml:mo><mml:mi>i</mml:mi><mml:mo>,</mml:mo><mml:mi>j</mml:mi><mml:mo>)</mml:mo><mml:mo>=</mml:mo><mml:mfrac><mml:mrow><mml:msubsup><mml:mi>Q</mml:mi><mml:mrow><mml:mtext>inter</mml:mtext></mml:mrow><mml:mrow><mml:mtext>raw</mml:mtext></mml:mrow></mml:msubsup><mml:mrow><mml:mo>(</mml:mo><mml:mrow><mml:mi>i</mml:mi><mml:mo>,</mml:mo><mml:mi>j</mml:mi></mml:mrow><mml:mo>)</mml:mo></mml:mrow></mml:mrow><mml:mrow><mml:mn>1</mml:mn><mml:mo>+</mml:mo><mml:msup><mml:mrow><mml:mrow><mml:mo>(</mml:mo><mml:mrow><mml:mfrac><mml:mrow><mml:msub><mml:mi>N</mml:mi><mml:mrow><mml:mtext>eff</mml:mtext></mml:mrow></mml:msub></mml:mrow><mml:mi>L</mml:mi></mml:mfrac></mml:mrow><mml:mo>)</mml:mo></mml:mrow></mml:mrow><mml:mrow><mml:mo>−</mml:mo><mml:mfrac><mml:mn>1</mml:mn><mml:mn>2</mml:mn></mml:mfrac></mml:mrow></mml:msup></mml:mrow></mml:mfrac></mml:mrow></mml:math></disp-formula>where <italic>N</italic><sub><italic>eff</italic></sub> is the effective number of sequences in the alignment after redundancy reduction, and L (total number of residues) is the length of the concatenated alignment. Previous work on single proteins has shown that the method requires a sufficient number of sequences in the alignment to be statistically meaningful. We thus filter for sequence sufficiency requiring <italic>N</italic><sub><italic>eff</italic></sub><italic>/L</italic> > 0.3 (<xref ref-type="table" rid="tbl1">Table 1</xref>, <xref ref-type="supplementary-material" rid="SD1-data SD2-data">Supplementary files 1 and 2</xref>). Predictions of coupled residues in the evaluation set were evaluated against their residue distances in known structures of protein pairs (<xref ref-type="bibr" rid="bib51">Rajagopala et al., 2014</xref>) (See <xref ref-type="supplementary-material" rid="SD7-data">Supplementary file 7</xref>) in order to determine the precision of the method.</p><p>To interpret the EVcomplex prediction of interaction between subunits a and b of the ATP synthase as well as UmuC and UmuD, individual monomer models were built de novo for the structurally unsolved a-subunit of ATP synthase and UmuC using the EVfold pipeline as previously published (<xref ref-type="bibr" rid="bib39">Marks et al., 2011</xref>; <xref ref-type="bibr" rid="bib24">Hopf et al., 2012</xref>). In both cases coupling parameters were calculated using PLM (<xref ref-type="bibr" rid="bib5">Balakrishnan et al., 2011</xref>; <xref ref-type="bibr" rid="bib18">Ekeberg et al., 2013</xref>) and sequences were clustered and weighted at 90% sequence identity (the resulting models are provided in ‘Supplementary data’).</p></sec><sec id="s4-5"><title>Prediction of interactions in a set of subunits</title><p>Following this same protocol EVcomplex scores were calculated for all possible 28 combinations of the 8 <italic>E. coli</italic> ATP synthase F<sub>0</sub> and F<sub>1</sub> subunits. Since we want to compare the computational predictions to some ‘ground truth’, as with the complexes for the rest of the manuscript, we used known 3D structures of the ATP synthase complex to assign whether or not the subunits interact (PDB: 3oaa, 1fs0, 2a7u; <xref ref-type="supplementary-material" rid="SD7-data">Supplementary file 7</xref>). Since we are also determining whether the subunits interact, not necessarily knowing full atomic detail residue interactions, we included subunit interactions that have been inferred from cryo-EM, crosslinking or other experiments, but do not necessarily have a crystal structure. These are represented as solid blue boxes, if the interaction is well established (<xref ref-type="bibr" rid="bib15">DeLeon-Rangel et al., 2013</xref>; <xref ref-type="bibr" rid="bib57">Schulenberg et al., 1999</xref>; <xref ref-type="bibr" rid="bib7">Brandt et al., 2013</xref>; <xref ref-type="bibr" rid="bib41">McLachlin and Dunn, 2000</xref>), or crosshatched blue if there is a lack of consensus in the community (<xref ref-type="fig" rid="fig6">Figure 6B</xref>, left panel).</p><p>For each possible interaction the EVcomplex score of the highest ranked inter-EC was considered as a proxy for the likelihood of interaction. Pairs with scores above 0.8 are considered likely to interact, between 0.75 and 0.8 weakly predicted, while interactions with scores below 0.75 are rejected as possible complexes (blue boxes, blue crosshatched, and white respectively in right panel of <xref ref-type="fig" rid="fig6">Figure 6B</xref>, and ‘Supplementary data’).</p></sec><sec id="s4-6"><title>Computation of 3D structure of complexes</title><p>A diverse set of 15 complexes was chosen from the 22 in the evaluation set that had at least 5 couplings above a complex score of 0.8 and was subsequently docked (<xref ref-type="supplementary-material" rid="SD3-data">Supplementary file 3</xref>). Proteins that have been crystallized together in a complex could bias the results of the docking, as they have complementary positions of the surface side chains. Therefore, where possible we used complexes that had a solved 3D structure of the unbound monomer, namely GcsH/GcsT, CyoA, FimC, DhaL, AtpE, PtqA/PtqB, RS10, and HK/RR, and in all other cases the side chains of the monomers were randomized either by using SCWRL4 (<xref ref-type="bibr" rid="bib35">Krivov et al., 2009</xref>) or restrained minimization with Schrodinger Protein Preparation Wizard (<xref ref-type="bibr" rid="bib55">Sastry et al., 2013</xref>) before docking. For ubiquinol oxidase (complex_054) the unbound structure of subunit 2 (CyoA) only covers the COX2 domain. In this case docking was performed using this unbound structure plus an additional run using the bound complex structure with perturbed side chains.</p><p>We used HADDOCK (<xref ref-type="bibr" rid="bib17">Dominguez et al., 2003</xref>), a widely used docking program based on ARIA (<xref ref-type="bibr" rid="bib37">Linge et al., 2003</xref>) and the CNS software (<xref ref-type="bibr" rid="bib8">Brunger, 2007</xref>) (Crystallography and NMR System), to dock the monomers for each protein pair with all inter-ECs with an EVcomplex score of 0.8 or above implemented as distance restraints on the α-carbon atoms of the backbone.</p><p>Each docking calculation starts with a rigid-body energy minimization, followed by semi-flexible refinement in torsion angle space, and ends with further refinement of the models in explicit solvent (water). 500/100/100 models generated for each of the 3 steps, respectively. All other parameters were left as the default values in the HADDOCK protocol. Each protein complex was run using predicted ECs as unambiguous distance restraints on the Cα atoms (d<sub>eff</sub> 5 Å, upper bound 2 Å, lower bound 2 Å; input files available in ‘Supplementary data’). As a negative control, each protein complex was also docked using center of mass restraints alone (ab initio docking mode of HADDOCK) (<xref ref-type="bibr" rid="bib13">de Vries et al., 2007</xref>) and in this case generating 10,000/500/500 models.</p><p>Each of the generated models is scored using a weighted sum of electrostatic (E<sub>elec</sub>) and van der Waals (E<sub>vdw</sub>) energies complemented by an empirical desolvation energy term (E<sub>desolv</sub>) (<xref ref-type="bibr" rid="bib20">Fernandez-Recio et al., 2004</xref>). The distance restraint energy term was explicitly removed from the equation in the last iteration (Edist3 = 0.0) to enable comparison of the scores between the runs that used a different number of ECs as distance restraints.</p></sec><sec id="s4-7"><title>Comparison of predicted to experimental structures</title><p>All computed models in the docked set were compared to the cognate crystal structures by the RMSD of all backbone atoms at the interface of the complex using ProFit v.3.1 (<ext-link ext-link-type="uri" xlink:href="http://www.bioinf.org.uk/software/profit/">http://www.bioinf.org.uk/software/profit/</ext-link>). The interface is defined as the set of all residues that contain any atom <6 Å away from any atom of the complex partner. For the AtpE–AtpG complex, we excluded the 2 C-terminal helices of AtpE as these helices are mobile and take many different positions relative to other ATP synthase subunits (<xref ref-type="bibr" rid="bib11">Cingolani and Duncan, 2011</xref>). Similarly, since the DHp domain of histidine kinases can take different positions relative to the CA domain, the HK-RR complex was compared over the interface between the DHp domain alone and the response regulator partner. In the case of the unbound ubiquinol oxidase docking results, only the interface between COX2 in subunit 2 and subunit 1 was considered. Accuracy of the computed models with EC restraints was compared with computed models with center of mass restraints alone (negative controls) (<xref ref-type="fig" rid="fig3s1">Figure 3—figure supplement 1</xref>, <xref ref-type="supplementary-material" rid="SD3-data">Supplementary file 3</xref>).</p><p>Data analysis was conducted primarily using IPython notebooks (<xref ref-type="bibr" rid="bib50">Perez and Granger, 2007</xref>). A webserver and all data are available at <ext-link ext-link-type="uri" xlink:href="http://EVcomplex.org">EVcomplex.org</ext-link> and the Dryad Digital Repository (<xref ref-type="bibr" rid="bib24a">Hopf et al., 2014</xref>).</p></sec><sec id="s4-8"><title>Supplementary Data</title><p>(Available at <ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5061/dryad.6t7b8">http://doi.org/10.5061/dryad.6t7b8</ext-link> [<xref ref-type="bibr" rid="bib24a">Hopf et al., 2014</xref>])</p><p>Supplementary data 1: Concatenated alignments for complexes predicted in this work</p><p>Supplementary data 2: Genome distance distribution of concatenated sequences per alignment</p><p>Supplementary data 3: EVcomplex predictions for evaluation and de novo set</p><p>Supplementary data 4: Docking input files and top 10 predicted models for evaluation set</p><p>Supplementary data 5: ATP synthase predictions, ATP synthase subunit a model</p><p>Supplementary data 6: UmuC model</p></sec></sec></body><back><sec sec-type="additional-information"><title>Additional information</title><fn-group content-type="competing-interest"><title>Competing interests</title><fn fn-type="conflict" id="conf1"><p>The authors declare that no competing interests exist.</p></fn></fn-group><fn-group content-type="author-contribution"><title>Author contributions</title><fn fn-type="con" id="con1"><p>TAH, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article</p></fn><fn fn-type="con" id="con2"><p>CPIS, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article</p></fn><fn fn-type="con" id="con3"><p>DSM, Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article</p></fn><fn fn-type="con" id="con4"><p>JPGLMR, Assisted docking in Haddock</p></fn><fn fn-type="con" id="con5"><p>AGG, Conducted comparison of ATP synthase subunit interactions</p></fn><fn fn-type="con" id="con6"><p>OK, Acquisition of data, Analysis and interpretation of data</p></fn><fn fn-type="con" id="con7"><p>CS, Conception and design, Drafting or revising the article</p></fn><fn fn-type="con" id="con8"><p>AMJJB, Provided expertise on Haddock docking protocols, Drafting or revising the article</p></fn></fn-group></sec><sec sec-type="supplementary-material"><title>Additional files</title><supplementary-material id="SD1-data"><object-id pub-id-type="doi">10.7554/eLife.03430.024</object-id><label>Supplementary file 1.</label><caption><p>Benchmark data set and results.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.024">http://dx.doi.org/10.7554/eLife.03430.024</ext-link></p></caption><media mime-subtype="xlsx" mimetype="application" xlink:href="elife03430s001.xlsx"/></supplementary-material><supplementary-material id="SD2-data"><object-id pub-id-type="doi">10.7554/eLife.03430.025</object-id><label>Supplementary file 2.</label><caption><p>De novo prediction data set and results.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.025">http://dx.doi.org/10.7554/eLife.03430.025</ext-link></p></caption><media mime-subtype="xlsx" mimetype="application" xlink:href="elife03430s002.xlsx"/></supplementary-material><supplementary-material id="SD3-data"><object-id pub-id-type="doi">10.7554/eLife.03430.026</object-id><label>Supplementary file 3.</label><caption><p>Docking results.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.026">http://dx.doi.org/10.7554/eLife.03430.026</ext-link></p></caption><media mime-subtype="xlsx" mimetype="application" xlink:href="elife03430s003.xlsx"/></supplementary-material><supplementary-material id="SD4-data"><object-id pub-id-type="doi">10.7554/eLife.03430.027</object-id><label>Supplementary file 4.</label><caption><p>Predicted inter-ECs for complexes in de novo prediction data set with EVcomplex score ≥0.8.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.027">http://dx.doi.org/10.7554/eLife.03430.027</ext-link></p></caption><media mime-subtype="xlsx" mimetype="application" xlink:href="elife03430s004.xlsx"/></supplementary-material><supplementary-material id="SD5-data"><object-id pub-id-type="doi">10.7554/eLife.03430.028</object-id><label>Supplementary file 5.</label><caption><p>ATP synthase interaction predictions.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.028">http://dx.doi.org/10.7554/eLife.03430.028</ext-link></p></caption><media mime-subtype="xlsx" mimetype="application" xlink:href="elife03430s005.xlsx"/></supplementary-material><supplementary-material id="SD6-data"><object-id pub-id-type="doi">10.7554/eLife.03430.029</object-id><label>Supplementary file 6.</label><caption><p>Comparison of ATP synthase EVcomplex predictions of a and b subunit with cross-linking studies.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.029">http://dx.doi.org/10.7554/eLife.03430.029</ext-link></p></caption><media mime-subtype="xlsx" mimetype="application" xlink:href="elife03430s006.xlsx"/></supplementary-material><supplementary-material id="SD7-data"><object-id pub-id-type="doi">10.7554/eLife.03430.030</object-id><label>Supplementary file 7.</label><caption><p>PDB identifiers used for comparison of predicted evolutionary couplings to known 3D structures.</p><p><bold>DOI:</bold> <ext-link ext-link-type="doi" xlink:href="10.7554/eLife.03430.030">http://dx.doi.org/10.7554/eLife.03430.030</ext-link></p></caption><media mime-subtype="txt" mimetype="text" xlink:href="elife03430s007.txt"/></supplementary-material><sec sec-type="datasets"><title>Major datasets</title><p>The following dataset was generated</p><p><related-object content-type="generated-dataset" source-id="http://dx.doi.org/10.5061/dryad.6t7b8" source-id-type="uri" id="dataro1"><collab collab-type="author">Hopf T</collab>, <collab collab-type="author">Schärfe C</collab>, <collab collab-type="author">Rodrigues J</collab>, <collab collab-type="author">Green A</collab>, <collab collab-type="author">Sander C</collab>, <collab collab-type="author">Bonvin A</collab>, <collab collab-type="author">Marks D</collab>, <year>2014</year><x>, </x><source>Data from: Sequence co-evolution gives 3D contacts and structures of protein complexes</source><x>, </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5061/dryad.6t7b8">http://dx.doi.org/10.5061/dryad.6t7b8</ext-link><x>, </x><comment>Publicly available at Dryad Digital Repository.</comment></related-object></p><p>The following previously published datasets were used:</p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1T36/pdb" source-id-type="uri" id="dataro2"><collab collab-type="author">Thoden JB</collab>, <collab collab-type="author">Huang X</collab>, <collab collab-type="author">Raushel FM</collab>, <collab collab-type="author">Holden HM</collab>, <year>2004</year><x>, </x><source>Crystal structure of E. coli carbamoyl phosphate synthetase small subunit mutant C248D complexed with uridine 5'-monophosphate</source><x>, </x><object-id pub-id-type="art-access-id">1T36</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1T36/pdb">http://dx.doi.org/10.2210/pdb1T36/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2QBA/pdb" source-id-type="uri" id="dataro3"><collab collab-type="author">Borovinskaya MA</collab>, <collab collab-type="author">Pai RD</collab>, <collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Schuwirth BS</collab>, <collab collab-type="author">Holton JM</collab>, <collab collab-type="author">Hirokawa G</collab>, <collab collab-type="author">Kaji H</collab>, <collab collab-type="author">Kaji A</collab>, <collab collab-type="author">Cate JHD</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin. This file contains the 50S subunit of the first 70S ribosome, with gentamicin bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400</source><x>, </x><object-id pub-id-type="art-access-id">2QBA</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2QBA/pdb">http://dx.doi.org/10.2210/pdb2QBA/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1KMI/pdb" source-id-type="uri" id="dataro4"><collab collab-type="author">Zhao R</collab>, <collab collab-type="author">Collins EJ</collab>, <collab collab-type="author">Bourret RB</collab>, <collab collab-type="author">Silversmith RE</collab>, <year>2001</year><x>, </x><source>Crystal Structure of an E.coli Chemotaxis Protein, Chez</source><x>, </x><object-id pub-id-type="art-access-id">1KMI</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1KMI/pdb">http://dx.doi.org/10.2210/pdb1KMI/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2QBB/pdb" source-id-type="uri" id="dataro5"><collab collab-type="author">Borovinskaya MA</collab>, <collab collab-type="author">Pai RD</collab>, <collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Schuwirth BS</collab>, <collab collab-type="author">Holton JM</collab>, <collab collab-type="author">Hirokawa G</collab>, <collab collab-type="author">Kaji H</collab>, <collab collab-type="author">Kaji A</collab>, <collab collab-type="author">Cate JHD</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin. This file contains the 30S subunit of the second 70S ribosome, with gentamicin bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400</source><x>, </x><object-id pub-id-type="art-access-id">2QBB</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2QBB/pdb">http://dx.doi.org/10.2210/pdb2QBB/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb4FHR/pdb" source-id-type="uri" id="dataro6"><collab collab-type="author">Paz A</collab>, <collab collab-type="author">Vartanian AS</collab>, <collab collab-type="author">Fortgang EA</collab>, <collab collab-type="author">Abramson J</collab>, <collab collab-type="author">Dahlquist FW</collab>, <year>2012</year><x>, </x><source>Crystal structure of the complex between the flagellar motor proteins FliG and FliM</source><x>, </x><object-id pub-id-type="art-access-id">4FHR</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb4FHR/pdb">http://dx.doi.org/10.2210/pdb4FHR/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2AW7/pdb" source-id-type="uri" id="dataro7"><collab collab-type="author">Schuwirth BS</collab>, <collab collab-type="author">Borovinskaya MA</collab>, <collab collab-type="author">Hau CW</collab>, <collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Vila-Sanjurjo A</collab>, <collab collab-type="author">Holton JM</collab>, <collab collab-type="author">Cate JHD</collab>, <year>2005</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli at 3.5 A resolution. This file contains the 30S subunit of the second 70S ribosome. The entire crystal structure contains two 70S ribosomes and is described in remark 400</source><x>, </x><object-id pub-id-type="art-access-id">2AW7</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2AW7/pdb">http://dx.doi.org/10.2210/pdb2AW7/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2AW4/pdb" source-id-type="uri" id="dataro8"><collab collab-type="author">Schuwirth BS</collab>, <collab collab-type="author">Borovinskaya MA</collab>, <collab collab-type="author">Hau CW</collab>, <collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Vila-Sanjurjo A</collab>, <collab collab-type="author">Holton JM</collab>, <collab collab-type="author">Cate JHD</collab>, <year>2005</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli at 3.5 A resolution. This file contains the 50S subunit of one 70S ribosome. The entire crystal structure contains two 70S ribosomes and is described in remark 400</source><x>, </x><object-id pub-id-type="art-access-id">2AW4</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2AW4/pdb">http://dx.doi.org/10.2210/pdb2AW4/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2QBF/pdb" source-id-type="uri" id="dataro9"><collab collab-type="author">Borovinskaya MA</collab>, <collab collab-type="author">Pai RD</collab>, <collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Schuwirth BS</collab>, <collab collab-type="author">Holton JM</collab>, <collab collab-type="author">Hirokawa G</collab>, <collab collab-type="author">Kaji H</collab>, <collab collab-type="author">Kaji A</collab>, <collab collab-type="author">Cate JHD</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with ribosome recycling factor (RRF). This file contains the 30S subunit of the second 70S ribosome. The entire crystal structure contains two 70S ribosomes and is described in remark 400</source><x>, </x><object-id pub-id-type="art-access-id">2QBF</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2QBF/pdb">http://dx.doi.org/10.2210/pdb2QBF/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2QBI/pdb" source-id-type="uri" id="dataro10"><collab collab-type="author">Borovinskaya MA</collab>, <collab collab-type="author">Pai RD</collab>, <collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Schuwirth BS</collab>, <collab collab-type="author">Holton JM</collab>, <collab collab-type="author">Hirokawa G</collab>, <collab collab-type="author">Kaji H</collab>, <collab collab-type="author">Kaji A</collab>, <collab collab-type="author">Cate JHD</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin and ribosome recycling factor (RRF). This file contains the 50S subunit of the first 70S ribosome, with gentamicin and RRF bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400</source><x>, </x><object-id pub-id-type="art-access-id">2QBI</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2QBI/pdb">http://dx.doi.org/10.2210/pdb2QBI/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2QBH/pdb" source-id-type="uri" id="dataro11"><collab collab-type="author">Borovinskaya MA</collab>, <collab collab-type="author">Pai RD</collab>, <collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Schuwirth BS</collab>, <collab collab-type="author">Holton JM</collab>, <collab collab-type="author">Hirokawa G</collab>, <collab collab-type="author">Kaji H</collab>, <collab collab-type="author">Kaji A</collab>, <collab collab-type="author">Cate JHD</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin and ribosome recycling factor (RRF). This file contains the 30S subunit of the first 70S ribosome, with gentamicin bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400</source><x>, </x><object-id pub-id-type="art-access-id">2QBH</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2QBH/pdb">http://dx.doi.org/10.2210/pdb2QBH/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2QBK/pdb" source-id-type="uri" id="dataro12"><collab collab-type="author">Borovinskaya MA</collab>, <collab collab-type="author">Pai RD</collab>, <collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Schuwirth BS</collab>, <collab collab-type="author">Holton JM</collab>, <collab collab-type="author">Hirokawa G</collab>, <collab collab-type="author">Kaji H</collab>, <collab collab-type="author">Kaji A</collab>, <collab collab-type="author">Cate JHD</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin and ribosome recycling factor (RRF). This file contains the 50S subunit of the second 70S ribosome, with gentamicin and RRF bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400</source><x>, </x><object-id pub-id-type="art-access-id">2QBK</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2QBK/pdb">http://dx.doi.org/10.2210/pdb2QBK/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2QBJ/pdb" source-id-type="uri" id="dataro13"><collab collab-type="author">Borovinskaya MA</collab>, <collab collab-type="author">Pai RD</collab>, <collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Schuwirth BS</collab>, <collab collab-type="author">Holton JM</collab>, <collab collab-type="author">Hirokawa G</collab>, <collab collab-type="author">Kaji H</collab>, <collab collab-type="author">Kaji A</collab>, <collab collab-type="author">Cate JHD</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin and ribosome recycling factor (RRF). This file contains the 30S subunit of the second 70S ribosome, with gentamicin bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400</source><x>, </x><object-id pub-id-type="art-access-id">2QBJ</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2QBJ/pdb">http://dx.doi.org/10.2210/pdb2QBJ/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3I1P/pdb" source-id-type="uri" id="dataro14"><collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Dunkle JA</collab>, <collab collab-type="author">Cate JHD</collab>, <year>2009</year><x>, </x><source>Crystal structure of the E. coli 70S ribosome in an intermediate state of ratcheting</source><x>, </x><object-id pub-id-type="art-access-id">3I1P</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3I1P/pdb">http://dx.doi.org/10.2210/pdb3I1P/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2QBC/pdb" source-id-type="uri" id="dataro15"><collab collab-type="author">Borovinskaya MA</collab>, <collab collab-type="author">Pai RD</collab>, <collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Schuwirth BS</collab>, <collab collab-type="author">Holton JM</collab>, <collab collab-type="author">Hirokawa G</collab>, <collab collab-type="author">Kaji H</collab>, <collab collab-type="author">Kaji A</collab>, <collab collab-type="author">Cate JHD</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin. This file contains the 50S subunit of the second 70S ribosome, with gentamicin bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400</source><x>, </x><object-id pub-id-type="art-access-id">2QBC</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2QBC/pdb">http://dx.doi.org/10.2210/pdb2QBC/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2WIU/pdb" source-id-type="uri" id="dataro16"><collab collab-type="author">Evdokimov A</collab>, <collab collab-type="author">Voznesensky I</collab>, <collab collab-type="author">Fennell K</collab>, <collab collab-type="author">Anderson M</collab>, <collab collab-type="author">Smith JF</collab>, <collab collab-type="author">Fisher DA</collab>, <year>2009</year><x>, </x><source>Mercury-modified bacterial persistence regulator hipBA</source><x>, </x><object-id pub-id-type="art-access-id">2WIU</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2WIU/pdb">http://dx.doi.org/10.2210/pdb2WIU/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2B76/pdb" source-id-type="uri" id="dataro17"><collab collab-type="author">Maklashina E</collab>, <collab collab-type="author">Iverson TM</collab>, <collab collab-type="author">Sher Y</collab>, <collab collab-type="author">Kotlyar V</collab>, <collab collab-type="author">Mirza O</collab>, <collab collab-type="author">Andrell J</collab>, <collab collab-type="author">Hudson JM</collab>, <collab collab-type="author">Armstrong FA</collab>, <collab collab-type="author">Cecchini G</collab>, <year>2005</year><x>, </x><source>E. coli Quinol fumarate reductase FrdA E49Q mutation</source><x>, </x><object-id pub-id-type="art-access-id">2B76</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2B76/pdb">http://dx.doi.org/10.2210/pdb2B76/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1IXR/pdb" source-id-type="uri" id="dataro18"><collab collab-type="author">Yamada K</collab>, <collab collab-type="author">Miyata T</collab>, <collab collab-type="author">Tsuchiya D</collab>, <collab collab-type="author">Oyama T</collab>, <collab collab-type="author">Fujiwara Y</collab>, <collab collab-type="author">Ohnishi T</collab>, <collab collab-type="author">Iwasaki H</collab>, <collab collab-type="author">Shinagawa H</collab>, <collab collab-type="author">Ariyoshi M</collab>, <collab collab-type="author">Mayanagi K</collab>, <collab collab-type="author">Morikawa K</collab>, <year>2002</year><x>, </x><source>RuvA-RuvB complex</source><x>, </x><object-id pub-id-type="art-access-id">1IXR</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1IXR/pdb">http://dx.doi.org/10.2210/pdb1IXR/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3IR7/pdb" source-id-type="uri" id="dataro19"><collab collab-type="author">Bertero MG</collab>, <collab collab-type="author">Rothery RA</collab>, <collab collab-type="author">Weiner JH</collab>, <collab collab-type="author">Strynadka NCJ</collab>, <year>2009</year><x>, </x><source>Crystal structure of NarGHI mutant NarG-R94S</source><x>, </x><object-id pub-id-type="art-access-id">3IR7</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3IR7/pdb">http://dx.doi.org/10.2210/pdb3IR7/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1BXR/pdb" source-id-type="uri" id="dataro20"><collab collab-type="author">Thoden JB</collab>, <collab collab-type="author">Wesenberg G</collab>, <collab collab-type="author">Raushel FM</collab>, <collab collab-type="author">Holden HM</collab>, <year>1998</year><x>, </x><source>Structure of Carbamoyl Phosphate Synthetase Complexed with the ATP Analog AMPPNP</source><x>, </x><object-id pub-id-type="art-access-id">1BXR</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1BXR/pdb">http://dx.doi.org/10.2210/pdb1BXR/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3DNV/pdb" source-id-type="uri" id="dataro21"><collab collab-type="author">Schumacher MA</collab>, <year>2008</year><x>, </x><source>MDT Protein</source><x>, </x><object-id pub-id-type="art-access-id">3DNV</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3DNV/pdb">http://dx.doi.org/10.2210/pdb3DNV/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb5AT1/pdb" source-id-type="uri" id="dataro22"><collab collab-type="author">Stevens RC</collab>, <collab collab-type="author">Gouaux JE</collab>, <collab collab-type="author">Lipscomb WN</collab>, <year>1990</year><x>, </x><source>Structural Consequences of Effector Binding to the T State of Aspartate Carbamoyltransferase. Crystal Structures of the Unligated and ATP-, and CTP-Complexed Enzymes AT 2.6-Angstroms Resolution</source><x>, </x><object-id pub-id-type="art-access-id">5AT1</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb5AT1/pdb">http://dx.doi.org/10.2210/pdb5AT1/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2AVY/pdb" source-id-type="uri" id="dataro23"><collab collab-type="author">Schuwirth BS</collab>, <collab collab-type="author">Borovinskaya MA</collab>, <collab collab-type="author">Hau CW</collab>, <collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Vila-Sanjurjo A</collab>, <collab collab-type="author">Holton JM</collab>, <collab collab-type="author">Cate JHD</collab>, <year>2005</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli at 3.5 A resolution. This file contains the 30S subunit of one 70S ribosome. The entire crystal structure contains two 70S ribosomes and is described in remark 400</source><x>, </x><object-id pub-id-type="art-access-id">2AVY</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2AVY/pdb">http://dx.doi.org/10.2210/pdb2AVY/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3K70/pdb" source-id-type="uri" id="dataro24"><collab collab-type="author">Saikrishnan K</collab>, <collab collab-type="author">Wigley DB</collab>, <year>2009</year><x>, </x><source>Crystal structure of the complete initiation complex of RecBCD</source><x>, </x><object-id pub-id-type="art-access-id">3K70</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3K70/pdb">http://dx.doi.org/10.2210/pdb3K70/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1KEE/pdb" source-id-type="uri" id="dataro25"><collab collab-type="author">Miles BW</collab>, <collab collab-type="author">Thoden JB</collab>, <collab collab-type="author">Holden HM</collab>, <collab collab-type="author">Raushel FM</collab>, <year>2001</year><x>, </x><source>Inactivation of the Amidotransferase Activity of Carbamoyl Phosphate Synthetase by the Antibiotic Acivicin</source><x>, </x><object-id pub-id-type="art-access-id">1KEE</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1KEE/pdb">http://dx.doi.org/10.2210/pdb1KEE/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2AVU/pdb" source-id-type="uri" id="dataro26"><collab collab-type="author">Wang S</collab>, <collab collab-type="author">Fleming RT</collab>, <collab collab-type="author">Westbrook EM</collab>, <collab collab-type="author">Matsumura P</collab>, <collab collab-type="author">McKay DB</collab>, <year>2005</year><x>, </x><source>Structure of the Escherichia coli FlhDC complex, a prokaryotic heteromeric regulator of transcription</source><x>, </x><object-id pub-id-type="art-access-id">2AVU</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2AVU/pdb">http://dx.doi.org/10.2210/pdb2AVU/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3TEH/pdb" source-id-type="uri" id="dataro27"><collab collab-type="author">Safro M</collab>, <collab collab-type="author">Klipcan L</collab>, <collab collab-type="author">Moor N</collab>, <year>2011</year><x>, </x><source>Crystal structure of Thermus thermophilus Phenylalanyl-tRNA synthetase comlexed with L-dopa</source><x>, </x><object-id pub-id-type="art-access-id">3TEH</object-id><x>; 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</x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2ATC/pdb">http://dx.doi.org/10.2210/pdb2ATC/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3SFS/pdb" source-id-type="uri" id="dataro37"><collab collab-type="author">Zhou J</collab>, <collab collab-type="author">Lancaster L</collab>, <collab collab-type="author">Trakhanov S</collab>, <collab collab-type="author">Noller HF</collab>, <year>2011</year><x>, </x><source>Crystal Structure of Release Factor RF3 Trapped in the GTP State on a Rotated Conformation of the Ribosome</source><x>, </x><object-id pub-id-type="art-access-id">3SFS</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3SFS/pdb">http://dx.doi.org/10.2210/pdb3SFS/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3N39/pdb" source-id-type="uri" id="dataro38"><collab collab-type="author">Boal AK</collab>, <collab collab-type="author">Cotruvo JA Jnr</collab>, <collab collab-type="author">Stubbe J</collab>, <collab collab-type="author">Rosenzweig AC</collab>, <year>2010</year><x>, </x><source>Ribonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli in Complex with NrdI</source><x>, </x><object-id pub-id-type="art-access-id">3N39</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3N39/pdb">http://dx.doi.org/10.2210/pdb3N39/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2FZG/pdb" source-id-type="uri" id="dataro39"><collab collab-type="author">Heng S</collab>, <collab collab-type="author">Stieglitz KA</collab>, <collab collab-type="author">Eldo J</collab>, <collab collab-type="author">Xia J</collab>, <collab collab-type="author">Cardia JP</collab>, <collab collab-type="author">Kantrowitz ER</collab>, <year>2006</year><x>, </x><source>The Structure of Wild-Type E. Coli Aspartate Transcarbamoylase in Complex with Novel T State Inhibitors at 2.25 Resolution</source><x>, </x><object-id pub-id-type="art-access-id">2FZG</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2FZG/pdb">http://dx.doi.org/10.2210/pdb2FZG/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3JWN/pdb" source-id-type="uri" id="dataro40"><collab collab-type="author">Le Trong I</collab>, <collab collab-type="author">Aprikian P</collab>, <collab collab-type="author">Stenkamp RE</collab>, <collab collab-type="author">Sokurenko EV</collab>, <year>2009</year><x>, </x><source>Complex of FimC, FimF, FimG and FimH</source><x>, </x><object-id pub-id-type="art-access-id">3JWN</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3JWN/pdb">http://dx.doi.org/10.2210/pdb3JWN/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3AO0/pdb" source-id-type="uri" id="dataro41"><collab collab-type="author">Shibata N</collab>, <year>2010</year><x>, </x><source>Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-CBL and (S)-2-amino-1-propanol</source><x>, </x><object-id pub-id-type="art-access-id">3AO0</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3AO0/pdb">http://dx.doi.org/10.2210/pdb3AO0/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2XDF/pdb" source-id-type="uri" id="dataro42"><collab collab-type="author">Schwieters CD</collab>, <collab collab-type="author">Suh JY</collab>, <collab collab-type="author">Grishaev A</collab>, <collab collab-type="author">Guirlando R</collab>, <collab collab-type="author">Takayama Y</collab>, <collab collab-type="author">Clore G.M</collab>, <year>2010</year><x>, </x><source>Solution Structure of the Enzyme I Dimer Complexed with HPr Using Residual Dipolar Couplings and Small Angle X-Ray Scattering</source><x>, </x><object-id pub-id-type="art-access-id">2XDF</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2XDF/pdb">http://dx.doi.org/10.2210/pdb2XDF/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3OFA/pdb" source-id-type="uri" id="dataro43"><collab collab-type="author">Dunkle JA</collab>, <collab collab-type="author">Xiong L</collab>, <collab collab-type="author">Mankin AS</collab>, <collab collab-type="author">Cate JHD</collab>, <year>2010</year><x>, </x><source>Crystal structure of the E. coli ribosome bound to chloramphenicol. 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This file contains the 30S subunit of the first 70S ribosome</source><x>, </x><object-id pub-id-type="art-access-id">3OFX</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3OFX/pdb">http://dx.doi.org/10.2210/pdb3OFX/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3OFY/pdb" source-id-type="uri" id="dataro50"><collab collab-type="author">Dunkle JA</collab>, <collab collab-type="author">Xiong L</collab>, <collab collab-type="author">Mankin AS</collab>, <collab collab-type="author">Cate JHD</collab>, <year>2010</year><x>, </x><source>Crystal structure of the E. coli ribosome bound to clindamycin. 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This file contains the 50S subunit of the first 70S ribosome bound to clindamycin</source><x>, </x><object-id pub-id-type="art-access-id">3OFZ</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3OFZ/pdb">http://dx.doi.org/10.2210/pdb3OFZ/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3OFP/pdb" source-id-type="uri" id="dataro52"><collab collab-type="author">Dunkle JA</collab>, <collab collab-type="author">Xiong L</collab>, <collab collab-type="author">Mankin AS</collab>, <collab collab-type="author">Cate JHD</collab>, <year>2010</year><x>, </x><source>Crystal structure of the E. coli ribosome bound to erythromycin. This file contains the 30S subunit of the second 70S ribosome</source><x>, </x><object-id pub-id-type="art-access-id">3OFP</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3OFP/pdb">http://dx.doi.org/10.2210/pdb3OFP/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1A0O/pdb" source-id-type="uri" id="dataro53"><collab collab-type="author">Chinardet N</collab>, <collab collab-type="author">Welch M</collab>, <collab collab-type="author">Mourey L</collab>, <collab collab-type="author">Birck C</collab>, <collab collab-type="author">Samama JP</collab>, <year>1997</year><x>, </x><source>Chey-binding domain of chea in complex with chey</source><x>, </x><object-id pub-id-type="art-access-id">1A0O</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1A0O/pdb">http://dx.doi.org/10.2210/pdb1A0O/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3OFR/pdb" source-id-type="uri" id="dataro54"><collab collab-type="author">Dunkle JA</collab>, <collab collab-type="author">Xiong L</collab>, <collab collab-type="author">Mankin AS</collab>, <collab collab-type="author">Cate JHD</collab>, <year>2010</year><x>, </x><source>Crystal structure of the E. coli ribosome bound to erythromycin. This file contains the 50S subunit of the first 70S ribosome with erthromycin bound</source><x>, </x><object-id pub-id-type="art-access-id">3OFR</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3OFR/pdb">http://dx.doi.org/10.2210/pdb3OFR/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2A0F/pdb" source-id-type="uri" id="dataro55"><collab collab-type="author">Stieglitz KA</collab>, <collab collab-type="author">Dusinberre KJ</collab>, <collab collab-type="author">Cardia JP</collab>, <collab collab-type="author">Tsuruta H</collab>, <collab collab-type="author">Kantrowitz ER</collab>, <year>2005</year><x>, </x><source>Structure of D236A mutant E. coli Aspartate Transcarbamoylase in presence of Phosphonoacetamide at 2.90 A resolution</source><x>, </x><object-id pub-id-type="art-access-id">2A0F</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2A0F/pdb">http://dx.doi.org/10.2210/pdb2A0F/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1AON/pdb" source-id-type="uri" id="dataro56"><collab collab-type="author">Xu Z</collab>, <collab collab-type="author">Horwich AL</collab>, <collab collab-type="author">Sigler PB</collab>, <year>1997</year><x>, </x><source>Crystal structure of the asymmetric chaperonin complex groel/groes/(ADP)7</source><x>, </x><object-id pub-id-type="art-access-id">1AON</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1AON/pdb">http://dx.doi.org/10.2210/pdb1AON/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2QP0/pdb" source-id-type="uri" id="dataro57"><collab collab-type="author">Borovinskaya MA</collab>, <collab collab-type="author">Shoji S</collab>, <collab collab-type="author">Holton JM</collab>, <collab collab-type="author">Fredrick K</collab>, <collab collab-type="author">Cate JHD</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with spectinomycin and neomycin. This file contains the 30S subunit of the second 70S ribosome, with spectinomycin and neomycin bound. The entire crystal structure contains two 70S ribosomes</source><x>, </x><object-id pub-id-type="art-access-id">2QP0</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2QP0/pdb">http://dx.doi.org/10.2210/pdb2QP0/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1GGR/pdb" source-id-type="uri" id="dataro58"><collab collab-type="author">Clore GM</collab>, <collab collab-type="author">Wang G</collab>, <year>2000</year><x>, </x><source>Complex of enzyme IIAGLC and the histidine-containing phosphocarrier protein HPR from Escherichia coli NMR, restrained regularized mean structure</source><x>, </x><object-id pub-id-type="art-access-id">1GGR</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1GGR/pdb">http://dx.doi.org/10.2210/pdb1GGR/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1FFS/pdb" source-id-type="uri" id="dataro59"><collab collab-type="author">Gouet P</collab>, <collab collab-type="author">Chinardet N</collab>, <collab collab-type="author">Welch M</collab>, <collab collab-type="author">Guillet V</collab>, <collab collab-type="author">Birck C</collab>, <collab collab-type="author">Mourey L</collab>, <collab collab-type="author">Samama JP</collab>, <year>2000</year><x>, </x><source>Chey-binding domain of chea in complex with chey from crystals soaked in acetyl phosphate</source><x>, </x><object-id pub-id-type="art-access-id">1FFS</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1FFS/pdb">http://dx.doi.org/10.2210/pdb1FFS/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3RFZ/pdb" source-id-type="uri" id="dataro60"><collab collab-type="author">Phan G</collab>, <collab collab-type="author">Remaut H</collab>, <collab collab-type="author">Lebedev A</collab>, <collab collab-type="author">Geibel S</collab>, <collab collab-type="author">Waksman G</collab>, <year>2011</year><x>, </x><source>Crystal structure of the FimD usher bound to its cognate FimC: FimH substrate</source><x>, </x><object-id pub-id-type="art-access-id">3RFZ</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3RFZ/pdb">http://dx.doi.org/10.2210/pdb3RFZ/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1KIU/pdb" source-id-type="uri" id="dataro61"><collab collab-type="author">Hung CS</collab>, <collab collab-type="author">Bouckaert J</collab>, <year>2001</year><x>, </x><source>FimH adhesin Q133N mutant-FimC chaperone complex with methyl-alpha-D-mannose</source><x>, </x><object-id pub-id-type="art-access-id">1KIU</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1KIU/pdb">http://dx.doi.org/10.2210/pdb1KIU/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2AWB/pdb" source-id-type="uri" id="dataro62"><collab collab-type="author">Schuwirth B.S</collab>, <collab collab-type="author">Borovinskaya M.A</collab>, <collab collab-type="author">Hau C.W</collab>, <collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Vila-Sanjurjo A</collab>, <collab collab-type="author">Holton J.M</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2005</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli at 3.5 A resolution. This file contains the 50S subunit of the second 70S ribosome. The entire crystal structure contains two 70S ribosomes and is described in remark 400</source><x>, </x><object-id pub-id-type="art-access-id">2AWB</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2AWB/pdb">http://dx.doi.org/10.2210/pdb2AWB/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1AT1/pdb" source-id-type="uri" id="dataro63"><collab collab-type="author">Gouaux J.E</collab>, <collab collab-type="author">Lipscomb W.N</collab>, <year>1989</year><x>, </x><source>CRYSTAL STRUCTURES OF PHOSPHONOACETAMIDE LIGATED T AND PHOSPHONOACETAMIDE AND MALONATE LIGATED R STATES OF ASPARTATE CARBAMOYLTRANSFERASE AT 2.8-ANGSTROMS RESOLUTION AND NEUTRAL P*H</source><x>, </x><object-id pub-id-type="art-access-id">1AT1</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1AT1/pdb">http://dx.doi.org/10.2210/pdb1AT1/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3PUZ/pdb" source-id-type="uri" id="dataro64"><collab collab-type="author">Oldham M.L</collab>, <collab collab-type="author">Chen J</collab>, <year>2010</year><x>, </x><source>Crystal Structure of a pre-translocation state MBP-Maltose transporter complex bound to AMP-PNP</source><x>, </x><object-id pub-id-type="art-access-id">3PUZ</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3PUZ/pdb">http://dx.doi.org/10.2210/pdb3PUZ/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3PUX/pdb" source-id-type="uri" id="dataro65"><collab collab-type="author">Oldham M.L</collab>, <collab collab-type="author">Chen J</collab>, <year>2010</year><x>, </x><source>Crystal Structure of an outward-facing MBP-Maltose transporter complex bound to ADP-BeF3</source><x>, </x><object-id pub-id-type="art-access-id">3PUX</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3PUX/pdb">http://dx.doi.org/10.2210/pdb3PUX/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3PUY/pdb" source-id-type="uri" id="dataro66"><collab collab-type="author">Oldham M.L</collab>, <collab collab-type="author">Chen J</collab>, <year>2010</year><x>, </x><source>Crystal Structure of an outward-facing MBP-Maltose transporter complex bound to AMP-PNP after crystal soaking of the pretranslocation state</source><x>, </x><object-id pub-id-type="art-access-id">3PUY</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3PUY/pdb">http://dx.doi.org/10.2210/pdb3PUY/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3PUV/pdb" source-id-type="uri" id="dataro67"><collab collab-type="author">Oldham M.L</collab>, <collab collab-type="author">Chen J</collab>, <year>2010</year><x>, </x><source>Crystal Structure of an outward-facing MBP-Maltose transporter complex bound to ADP-VO4</source><x>, </x><object-id pub-id-type="art-access-id">3PUV</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3PUV/pdb">http://dx.doi.org/10.2210/pdb3PUV/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3PUW/pdb" source-id-type="uri" id="dataro68"><collab collab-type="author">Oldham M.L</collab>, <collab collab-type="author">Chen J</collab>, <year>2010</year><x>, </x><source>Crystal Structure of an outward-facing MBP-Maltose transporter complex bound to ADP-AlF4</source><x>, </x><object-id pub-id-type="art-access-id">3PUW</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3PUW/pdb">http://dx.doi.org/10.2210/pdb3PUW/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2H3E/pdb" source-id-type="uri" id="dataro69"><collab collab-type="author">Eldo J</collab>, <collab collab-type="author">Cardia J.P</collab>, <collab collab-type="author">O'Day E.M</collab>, <collab collab-type="author">Xia J</collab>, <collab collab-type="author">Tsuruta H</collab>, <collab collab-type="author">Kantrowitz E.R</collab>, <year>2006</year><x>, </x><source>Structure of wild-type E. coli Aspartate Transcarbamoylase in the presence of N-phosphonacetyl-L-isoasparagine at 2.3A resolution</source><x>, </x><object-id pub-id-type="art-access-id">2H3E</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2H3E/pdb">http://dx.doi.org/10.2210/pdb2H3E/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3OG0/pdb" source-id-type="uri" id="dataro70"><collab collab-type="author">Dunkle J.A</collab>, <collab collab-type="author">Xiong L</collab>, <collab collab-type="author">Mankin A.S</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2010</year><x>, </x><source>Crystal structure of the E. coli ribosome bound to clindamycin. This file contains the 50S subunit of the second 70S ribosome</source><x>, </x><object-id pub-id-type="art-access-id">3OG0</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3OG0/pdb">http://dx.doi.org/10.2210/pdb3OG0/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb4AT1/pdb" source-id-type="uri" id="dataro71"><collab collab-type="author">Stevens R.C</collab>, <collab collab-type="author">Gouaux J.E</collab>, <collab collab-type="author">Lipscomb W.N</collab>, <year>1990</year><x>, </x><source>STRUCTURAL CONSEQUENCES OF EFFECTOR BINDING TO THE T STATE OF ASPARTATE CARBAMOYLTRANSFERASE. CRYSTAL STRUCTURES OF THE UNLIGATED AND ATP-, AND CTP-COMPLEXED ENZYMES AT 2.6-ANGSTROMS RESOLUTION</source><x>, </x><object-id pub-id-type="art-access-id">4AT1</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb4AT1/pdb">http://dx.doi.org/10.2210/pdb4AT1/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2Z4M/pdb" source-id-type="uri" id="dataro72"><collab collab-type="author">Borovinskaya M.A</collab>, <collab collab-type="author">Pai R.D</collab>, <collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Schuwirth B.-S</collab>, <collab collab-type="author">Holton J.M</collab>, <collab collab-type="author">Hirokawa G</collab>, <collab collab-type="author">Kaji H</collab>, <collab collab-type="author">Kaji A</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with paromomycin and ribosome recycling factor (RRF). This file contains the 30S subunit of the second 70S ribosome, with paromomycin bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400</source><x>, </x><object-id pub-id-type="art-access-id">2Z4M</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2Z4M/pdb">http://dx.doi.org/10.2210/pdb2Z4M/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2WDQ/pdb" source-id-type="uri" id="dataro73"><collab collab-type="author">Ruprecht J</collab>, <collab collab-type="author">Yankovskaya V</collab>, <collab collab-type="author">Maklashina E</collab>, <collab collab-type="author">Iwata S</collab>, <collab collab-type="author">Cecchini G</collab>, <year>2009</year><x>, </x><source>E. coli succinate:quinone oxidoreductase (SQR) with carboxin bound</source><x>, </x><object-id pub-id-type="art-access-id">2WDQ</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2WDQ/pdb">http://dx.doi.org/10.2210/pdb2WDQ/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1JDB/pdb" source-id-type="uri" id="dataro74"><collab collab-type="author">Thoden J.B</collab>, <collab collab-type="author">Holden H.M</collab>, <collab collab-type="author">Wesenberg G</collab>, <collab collab-type="author">Raushel F.M</collab>, <collab collab-type="author">Rayment I</collab>, <year>1997</year><x>, </x><source>CARBAMOYL PHOSPHATE SYNTHETASE FROM ESCHERICHIA COLI</source><x>, </x><object-id pub-id-type="art-access-id">1JDB</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1JDB/pdb">http://dx.doi.org/10.2210/pdb1JDB/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2WP9/pdb" source-id-type="uri" id="dataro75"><collab collab-type="author">Ruprecht J</collab>, <collab collab-type="author">Yankovskaya V</collab>, <collab collab-type="author">Maklashina E</collab>, <collab collab-type="author">Iwata S</collab>, <collab collab-type="author">Cecchini G</collab>, <year>2009</year><x>, </x><source>Crystal structure of the E. coli succinate:quinone oxidoreductase ( SQR) SdhB His207Thr mutant</source><x>, </x><object-id pub-id-type="art-access-id">2WP9</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2WP9/pdb">http://dx.doi.org/10.2210/pdb2WP9/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2D1P/pdb" source-id-type="uri" id="dataro76"><collab collab-type="author">Numata T</collab>, <collab collab-type="author">Fukai S</collab>, <collab collab-type="author">Ikeuchi Y</collab>, <collab collab-type="author">Suzuki T</collab>, <collab collab-type="author">Nureki O</collab>, <year>2005</year><x>, </x><source>crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification</source><x>, </x><object-id pub-id-type="art-access-id">2D1P</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2D1P/pdb">http://dx.doi.org/10.2210/pdb2D1P/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3I1O/pdb" source-id-type="uri" id="dataro77"><collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Dunkle J.A</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2009</year><x>, </x><source>Crystal structure of the E. coli 70S ribosome in an intermediate state of ratcheting</source><x>, </x><object-id pub-id-type="art-access-id">3I1O</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3I1O/pdb">http://dx.doi.org/10.2210/pdb3I1O/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3I1N/pdb" source-id-type="uri" id="dataro78"><collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Dunkle J.A</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2009</year><x>, </x><source>Crystal structure of the E. coli 70S ribosome in an intermediate state of ratcheting</source><x>, </x><object-id pub-id-type="art-access-id">3I1N</object-id><x>; 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The entire crystal structure contains two 70S ribosomes</source><x>, </x><object-id pub-id-type="art-access-id">2QOU</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2QOU/pdb">http://dx.doi.org/10.2210/pdb2QOU/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2AT1/pdb" source-id-type="uri" id="dataro93"><collab collab-type="author">Gouaux J.E</collab>, <collab collab-type="author">Lipscomb W.N</collab>, <year>1989</year><x>, </x><source>CRYSTAL STRUCTURES OF PHOSPHONOACETAMIDE LIGATED T AND PHOSPHONOACETAMIDE AND MALONATE LIGATED R STATES OF ASPARTATE CARBAMOYLTRANSFERASE AT 2.8-ANGSTROMS RESOLUTION AND NEUTRAL PH</source><x>, </x><object-id pub-id-type="art-access-id">2AT1</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2AT1/pdb">http://dx.doi.org/10.2210/pdb2AT1/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1FFG/pdb" source-id-type="uri" id="dataro94"><collab collab-type="author">Gouet P</collab>, <collab collab-type="author">Chinardet N</collab>, <collab collab-type="author">Welch M</collab>, <collab collab-type="author">Guillet V</collab>, <collab collab-type="author">Birck C</collab>, <collab collab-type="author">Mourey L</collab>, <collab collab-type="author">Samama J.-P</collab>, <year>2000</year><x>, </x><source>CHEY-BINDING DOMAIN OF CHEA IN COMPLEX WITH CHEY AT 2.1 A RESOLUTION</source><x>, </x><object-id pub-id-type="art-access-id">1FFG</object-id><x>; 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</x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2IPO/pdb">http://dx.doi.org/10.2210/pdb2IPO/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb4HEA/pdb" source-id-type="uri" id="dataro98"><collab collab-type="author">Baradaran R</collab>, <collab collab-type="author">Berrisford J.M</collab>, <collab collab-type="author">Minhas G.S</collab>, <collab collab-type="author">Sazanov L.A</collab>, <year>2012</year><x>, </x><source>Crystal structure of the entire respiratory complex I from Thermus thermophilus</source><x>, </x><object-id pub-id-type="art-access-id">4HEA</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb4HEA/pdb">http://dx.doi.org/10.2210/pdb4HEA/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2VHM/pdb" source-id-type="uri" id="dataro99"><collab collab-type="author">Bingel-Erlenmeyer R</collab>, <collab collab-type="author">Kohler R</collab>, <collab collab-type="author">Kramer G</collab>, <collab collab-type="author">Sandikci A</collab>, <collab collab-type="author">Antolic S</collab>, <collab collab-type="author">Maier T</collab>, <collab collab-type="author">Schaffitzel C</collab>, <collab collab-type="author">Wiedmann B</collab>, <collab collab-type="author">Bukau B</collab>, <collab collab-type="author">Ban N</collab>, <year>2007</year><x>, </x><source>Structure of PDF binding helix in complex with the ribosome</source><x>, </x><object-id pub-id-type="art-access-id">2VHM</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2VHM/pdb">http://dx.doi.org/10.2210/pdb2VHM/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1QUN/pdb" source-id-type="uri" id="dataro100"><collab collab-type="author">Choudhury D</collab>, <collab collab-type="author">Thompson A</collab>, <collab collab-type="author">Stojanoff V</collab>, <collab collab-type="author">Langerman S</collab>, <collab collab-type="author">Pinkner J</collab>, <collab collab-type="author">Hultgren S.J</collab>, <collab collab-type="author">Knight S</collab>, <year>1999</year><x>, </x><source>X-RAY STRUCTURE OF THE FIMC-FIMH CHAPERONE ADHESIN COMPLEX FROM UROPATHOGENIC E.COLI</source><x>, </x><object-id pub-id-type="art-access-id">1QUN</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1QUN/pdb">http://dx.doi.org/10.2210/pdb1QUN/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2QGF/pdb" source-id-type="uri" id="dataro102"><collab collab-type="author">Stec B</collab>, <collab collab-type="author">Williams M.K</collab>, <collab collab-type="author">Stieglitz K.A</collab>, <collab collab-type="author">Kantrowitz E.R</collab>, <year>2007</year><x>, </x><source>Structure of regulatory chain mutant H20A of asparate transcarbamoylase from E. coli</source><x>, </x><object-id pub-id-type="art-access-id">2QGF</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2QGF/pdb">http://dx.doi.org/10.2210/pdb2QGF/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1SIW/pdb" source-id-type="uri" id="dataro103"><collab collab-type="author">Rothery R.A</collab>, <collab collab-type="author">Bertero M.G</collab>, <collab collab-type="author">Cammack R</collab>, <collab collab-type="author">Palak M</collab>, <collab collab-type="author">Blasco F</collab>, <collab collab-type="author">Strynadka N.C</collab>, <collab collab-type="author">Weiner J.H</collab>, <year>2004</year><x>, </x><source>Crystal structure of the apomolybdo-NarGHI</source><x>, </x><object-id pub-id-type="art-access-id">1SIW</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1SIW/pdb">http://dx.doi.org/10.2210/pdb1SIW/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1NEK/pdb" source-id-type="uri" id="dataro104"><collab collab-type="author">Yankovskaya V</collab>, <collab collab-type="author">Horsefield R</collab>, <collab collab-type="author">Tornroth S</collab>, <collab collab-type="author">Luna-Chavez C</collab>, <collab collab-type="author">Miyoshi H</collab>, <collab collab-type="author">Leger C</collab>, <collab collab-type="author">Byrne B</collab>, <collab collab-type="author">Cecchini G</collab>, <collab collab-type="author">Iwata S</collab>, <year>2002</year><x>, </x><source>Complex II (Succinate Dehydrogenase) From E. Coli with ubiquinone bound</source><x>, </x><object-id pub-id-type="art-access-id">1NEK</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1NEK/pdb">http://dx.doi.org/10.2210/pdb1NEK/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1FFT/pdb" source-id-type="uri" id="dataro105"><collab collab-type="author">Abramson J</collab>, <collab collab-type="author">Riistama S</collab>, <collab collab-type="author">Larsson G</collab>, <collab collab-type="author">Jasaitis A</collab>, <collab collab-type="author">Svensson-Ek M</collab>, <collab collab-type="author">Puustinen A</collab>, <collab collab-type="author">Iwata S</collab>, <collab collab-type="author">Wikstrom M</collab>, <year>2000</year><x>, </x><source>The structure of ubiquinol oxidase from Escherichia E. coli</source><x>, </x><object-id pub-id-type="art-access-id">1FFT</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1FFT/pdb">http://dx.doi.org/10.2210/pdb1FFT/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1NEN/pdb" source-id-type="uri" id="dataro106"><collab collab-type="author">Yankovskaya V</collab>, <collab collab-type="author">Horsefield R</collab>, <collab collab-type="author">Tornroth S</collab>, <collab collab-type="author">Luna-Chavez C</collab>, <collab collab-type="author">Miyoshi H</collab>, <collab collab-type="author">Leger C</collab>, <collab collab-type="author">Byrne B</collab>, <collab collab-type="author">Cecchini G</collab>, <collab collab-type="author">Iwata S</collab>, <year>2002</year><x>, </x><source>Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 inhibitor co-crystallized at the ubiquinone binding site</source><x>, </x><object-id pub-id-type="art-access-id">1NEN</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1NEN/pdb">http://dx.doi.org/10.2210/pdb1NEN/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1R6Q/pdb" source-id-type="uri" id="dataro107"><collab collab-type="author">Xia D</collab>, <collab collab-type="author">Maurizi M.R</collab>, <collab collab-type="author">Guo F</collab>, <collab collab-type="author">Singh S.K</collab>, <collab collab-type="author">Esser L</collab>, <year>2003</year><x>, </x><source>ClpNS with fragments</source><x>, </x><object-id pub-id-type="art-access-id">1R6Q</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1R6Q/pdb">http://dx.doi.org/10.2210/pdb1R6Q/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2WDR/pdb" source-id-type="uri" id="dataro108"><collab collab-type="author">Ruprecht J</collab>, <collab collab-type="author">Yankovskaya V</collab>, <collab collab-type="author">Maklashina E</collab>, <collab collab-type="author">Iwata S</collab>, <collab collab-type="author">Cecchini G</collab>, <year>2009</year><x>, </x><source>E. coli succinate:quinone oxidoreductase (SQR) with pentachlorophenol bound</source><x>, </x><object-id pub-id-type="art-access-id">2WDR</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2WDR/pdb">http://dx.doi.org/10.2210/pdb2WDR/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2QG9/pdb" source-id-type="uri" id="dataro109"><collab collab-type="author">Stec B</collab>, <collab collab-type="author">Williams M.K</collab>, <collab collab-type="author">Stieglitz K.A</collab>, <collab collab-type="author">Kantrowitz E.R</collab>, <year>2007</year><x>, </x><source>Structure of a regulatory subunit mutant D19A of ATCase from E. coli</source><x>, </x><object-id pub-id-type="art-access-id">2QG9</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2QG9/pdb">http://dx.doi.org/10.2210/pdb2QG9/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3HZI/pdb" source-id-type="uri" id="dataro110"><collab collab-type="author">Schumacher M.A</collab>, <year>2009</year><x>, </x><source>Structure of mdt protein</source><x>, </x><object-id pub-id-type="art-access-id">3HZI</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3HZI/pdb">http://dx.doi.org/10.2210/pdb3HZI/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3TUZ/pdb" source-id-type="uri" id="dataro111"><collab collab-type="author">Johnson E</collab>, <collab collab-type="author">Nguyen P</collab>, <collab collab-type="author">Rees D.C</collab>, <year>2011</year><x>, </x><source>Inward facing conformations of the MetNI methionine ABC transporter: CY5 SeMet soak crystal form</source><x>, </x><object-id pub-id-type="art-access-id">3TUZ</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3TUZ/pdb">http://dx.doi.org/10.2210/pdb3TUZ/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1NVM/pdb" source-id-type="uri" id="dataro112"><collab collab-type="author">Manjasetty A.B</collab>, <collab collab-type="author">Powlowski J</collab>, <collab collab-type="author">Vrielink A</collab>, <year>2003</year><x>, </x><source>Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate</source><x>, </x><object-id pub-id-type="art-access-id">1NVM</object-id><x>; 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(Structure 2 of 4)</source><x>, </x><object-id pub-id-type="art-access-id">2VHN</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2VHN/pdb">http://dx.doi.org/10.2210/pdb2VHN/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2QB9/pdb" source-id-type="uri" id="dataro117"><collab collab-type="author">Borovinskaya M.A</collab>, <collab collab-type="author">Pai R.D</collab>, <collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Schuwirth B.-S</collab>, <collab collab-type="author">Holton J.M</collab>, <collab collab-type="author">Hirokawa G</collab>, <collab collab-type="author">Kaji H</collab>, <collab collab-type="author">Kaji A</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with gentamicin. This file contains the 30S subunit of the first 70S ribosome, with gentamicin bound. 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This file contains the 50S subunit of the first 70S ribosome bound to CEM-101</source><x>, </x><object-id pub-id-type="art-access-id">3ORB</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3ORB/pdb">http://dx.doi.org/10.2210/pdb3ORB/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb7AT1/pdb" source-id-type="uri" id="dataro148"><collab collab-type="author">Gouaux J.E</collab>, <collab collab-type="author">Stevens R.C</collab>, <collab collab-type="author">Lipscomb W.N</collab>, <year>1989</year><x>, </x><source>CRYSTAL STRUCTURES OF ASPARTATE CARBAMOYLTRANSFERASE LIGATED WITH PHOSPHONOACETAMIDE, MALONATE, AND CTP OR ATP AT 2.8-ANGSTROMS RESOLUTION AND NEUTRAL P*H</source><x>, </x><object-id pub-id-type="art-access-id">7AT1</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb7AT1/pdb">http://dx.doi.org/10.2210/pdb7AT1/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1Y4Z/pdb" source-id-type="uri" id="dataro149"><collab collab-type="author">Bertero M.G</collab>, <collab collab-type="author">Rothery R.A</collab>, <collab collab-type="author">Boroumand N</collab>, <collab collab-type="author">Palak M</collab>, <collab collab-type="author">Blasco F</collab>, <collab collab-type="author">Ginet N</collab>, <collab collab-type="author">Weiner J.H</collab>, <collab collab-type="author">Strynadka N.C.J</collab>, <year>2004</year><x>, </x><source>The crystal structure of Nitrate Reductase A, NarGHI, in complex with the Q-site inhibitor pentachlorophenol</source><x>, </x><object-id pub-id-type="art-access-id">1Y4Z</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1Y4Z/pdb">http://dx.doi.org/10.2210/pdb1Y4Z/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3I22/pdb" source-id-type="uri" id="dataro150"><collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Dunkle J.A</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2009</year><x>, </x><source>Crystal structure of the E. coli 70S ribosome in an intermediate state of ratcheting</source><x>, </x><object-id pub-id-type="art-access-id">3I22</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3I22/pdb">http://dx.doi.org/10.2210/pdb3I22/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1FM0/pdb" source-id-type="uri" id="dataro151"><collab collab-type="author">Rudolph M.J</collab>, <collab collab-type="author">Wuebbens M.M</collab>, <collab collab-type="author">Rajagolpalan K.V</collab>, <collab collab-type="author">Schindelin H</collab>, <year>2000</year><x>, </x><source>MOLYBDOPTERIN SYNTHASE (MOAD/MOAE)</source><x>, </x><object-id pub-id-type="art-access-id">1FM0</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1FM0/pdb">http://dx.doi.org/10.2210/pdb1FM0/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3TUI/pdb" source-id-type="uri" id="dataro152"><collab collab-type="author">Johnson E</collab>, <collab collab-type="author">Nguyen P.T</collab>, <collab collab-type="author">Rees D.C</collab>, <year>2011</year><x>, </x><source>Inward facing conformations of the MetNI methionine ABC transporter: CY5 native crystal form</source><x>, </x><object-id pub-id-type="art-access-id">3TUI</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3TUI/pdb">http://dx.doi.org/10.2210/pdb3TUI/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2FZK/pdb" source-id-type="uri" id="dataro153"><collab collab-type="author">Heng S</collab>, <collab collab-type="author">Stieglitz K.A</collab>, <collab collab-type="author">Eldo J</collab>, <collab collab-type="author">Xia J</collab>, <collab collab-type="author">Cardia J.P</collab>, <collab collab-type="author">Kantrowitz E.R</collab>, <year>2006</year><x>, </x><source>The Structure of Wild-Type E. Coli Aspartate Transcarbamoylase in Complex with Novel T State Inhibitors at 2.50 Resolution</source><x>, </x><object-id pub-id-type="art-access-id">2FZK</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2FZK/pdb">http://dx.doi.org/10.2210/pdb2FZK/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1MG9/pdb" source-id-type="uri" id="dataro154"><collab collab-type="author">Zeth K</collab>, <collab collab-type="author">Ravelli R.B</collab>, <collab collab-type="author">Paal K</collab>, <collab collab-type="author">Cusack S</collab>, <collab collab-type="author">Bukau B</collab>, <collab collab-type="author">Dougan D.A</collab>, <year>2002</year><x>, </x><source>The structural basis of ClpS-mediated switch in ClpA substrate recognition</source><x>, </x><object-id pub-id-type="art-access-id">1MG9</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1MG9/pdb">http://dx.doi.org/10.2210/pdb1MG9/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb4GD2/pdb" source-id-type="uri" id="dataro155"><collab collab-type="author">Dunkle J.A</collab>, <collab collab-type="author">Wang L</collab>, <collab collab-type="author">Feldman M.B</collab>, <collab collab-type="author">Pulk A</collab>, <collab collab-type="author">Chen V.B</collab>, <collab collab-type="author">Kapral G.J</collab>, <collab collab-type="author">Noeske J</collab>, <collab collab-type="author">Richardson J.S</collab>, <collab collab-type="author">Blanchard S.C</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2012</year><x>, </x><source>Structures of the bacterial ribosome in classical and hybrid states of tRNA binding</source><x>, </x><object-id pub-id-type="art-access-id">4GD2</object-id><x>; 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</x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3IR6/pdb">http://dx.doi.org/10.2210/pdb3IR6/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3I20/pdb" source-id-type="uri" id="dataro158"><collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Dunkle J.A</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2009</year><x>, </x><source>Crystal structure of the E. coli 70S ribosome in an intermediate state of ratcheting</source><x>, </x><object-id pub-id-type="art-access-id">3I20</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3I20/pdb">http://dx.doi.org/10.2210/pdb3I20/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3I21/pdb" source-id-type="uri" id="dataro159"><collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Dunkle J.A</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2009</year><x>, </x><source>Crystal structure of the E. coli 70S ribosome in an intermediate state of ratcheting</source><x>, </x><object-id pub-id-type="art-access-id">3I21</object-id><x>; 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This file contains the 30S subunit of the first 70S ribosome, with neomycin bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400</source><x>, </x><object-id pub-id-type="art-access-id">2QAL</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2QAL/pdb">http://dx.doi.org/10.2210/pdb2QAL/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2QAM/pdb" source-id-type="uri" id="dataro161"><collab collab-type="author">Borovinskaya M.A</collab>, <collab collab-type="author">Pai R.D</collab>, <collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Schuwirth B.-S</collab>, <collab collab-type="author">Holton J.M</collab>, <collab collab-type="author">Hirokawa G</collab>, <collab collab-type="author">Kaji H</collab>, <collab collab-type="author">Kaji A</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with neomycin. This file contains the 50S subunit of the first 70S ribosome, with neomycin bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400</source><x>, </x><object-id pub-id-type="art-access-id">2QAM</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2QAM/pdb">http://dx.doi.org/10.2210/pdb2QAM/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2QAN/pdb" source-id-type="uri" id="dataro162"><collab collab-type="author">Borovinskaya M.A</collab>, <collab collab-type="author">Pai R.D</collab>, <collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Schuwirth B.-S</collab>, <collab collab-type="author">Holton J.M</collab>, <collab collab-type="author">Hirokawa G</collab>, <collab collab-type="author">Kaji H</collab>, <collab collab-type="author">Kaji A</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with neomycin. This file contains the 30S subunit of the second 70S ribosome, with neomycin bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400</source><x>, </x><object-id pub-id-type="art-access-id">2QAN</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2QAN/pdb">http://dx.doi.org/10.2210/pdb2QAN/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3D7S/pdb" source-id-type="uri" id="dataro163"><collab collab-type="author">Stieglitz K.A</collab>, <collab collab-type="author">Xia J</collab>, <collab collab-type="author">Kantrowitz E.R</collab>, <year>2008</year><x>, </x><source>Crystal structure of Wild-Type E. Coli Asparate Transcarbamoylase at pH 8.5 at 2.80 A Resolution</source><x>, </x><object-id pub-id-type="art-access-id">3D7S</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3D7S/pdb">http://dx.doi.org/10.2210/pdb3D7S/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2Z4L/pdb" source-id-type="uri" id="dataro164"><collab collab-type="author">Borovinskaya M.A</collab>, <collab collab-type="author">Pai R.D</collab>, <collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Schuwirth B.-S</collab>, <collab collab-type="author">Holton J.M</collab>, <collab collab-type="author">Hirokawa G</collab>, <collab collab-type="author">Kaji H</collab>, <collab collab-type="author">Kaji A</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with paromomycin and ribosome recycling factor (RRF). This file contains the 50S subunit of the first 70S ribosome, with paromomycin and RRF bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400</source><x>, </x><object-id pub-id-type="art-access-id">2Z4L</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2Z4L/pdb">http://dx.doi.org/10.2210/pdb2Z4L/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb9ATC/pdb" source-id-type="uri" id="dataro165"><collab collab-type="author">Ha Y</collab>, <collab collab-type="author">Allewell N.M</collab>, <year>1998</year><x>, </x><source>ATCASE Y165F MUTANT</source><x>, </x><object-id pub-id-type="art-access-id">9ATC</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb9ATC/pdb">http://dx.doi.org/10.2210/pdb9ATC/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2Z4N/pdb" source-id-type="uri" id="dataro166"><collab collab-type="author">Borovinskaya M.A</collab>, <collab collab-type="author">Pai R.D</collab>, <collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Schuwirth B.-S</collab>, <collab collab-type="author">Holton J.M</collab>, <collab collab-type="author">Hirokawa G</collab>, <collab collab-type="author">Kaji H</collab>, <collab collab-type="author">Kaji A</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with paromomycin and ribosome recycling factor (RRF). This file contains the 50S subunit of the second 70S ribosome, with paromomycin and RRF bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400</source><x>, </x><object-id pub-id-type="art-access-id">2Z4N</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2Z4N/pdb">http://dx.doi.org/10.2210/pdb2Z4N/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2QOZ/pdb" source-id-type="uri" id="dataro167"><collab collab-type="author">Borovinskaya M.A</collab>, <collab collab-type="author">Shoji S</collab>, <collab collab-type="author">Holton J.M</collab>, <collab collab-type="author">Fredrick K</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with spectinomycin and neomycin. This file contains the 50S subunit of the first 70S ribosome, with neomycin bound. The entire crystal structure contains two 70S ribosomes</source><x>, </x><object-id pub-id-type="art-access-id">2QOZ</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2QOZ/pdb">http://dx.doi.org/10.2210/pdb2QOZ/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2Z4K/pdb" source-id-type="uri" id="dataro168"><collab collab-type="author">Borovinskaya M.A</collab>, <collab collab-type="author">Pai R.D</collab>, <collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Schuwirth B.-S</collab>, <collab collab-type="author">Holton J.M</collab>, <collab collab-type="author">Hirokawa G</collab>, <collab collab-type="author">Kaji H</collab>, <collab collab-type="author">Kaji A</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with paromomycin and ribosome recycling factor (RRF). This file contains the 30S subunit of the first 70S ribosome, with paromomycin bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400</source><x>, </x><object-id pub-id-type="art-access-id">2Z4K</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2Z4K/pdb">http://dx.doi.org/10.2210/pdb2Z4K/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb6AT1/pdb" source-id-type="uri" id="dataro169"><collab collab-type="author">Stevens R.C</collab>, <collab collab-type="author">Gouaux J.E</collab>, <collab collab-type="author">Lipscomb W.N</collab>, <year>1990</year><x>, </x><source>Structural consequences of effector binding to the t state of aspartate carbamoyltransferase. Crystal structures of the unligated and atp-, and ctp-complexed enzymes at 2.6-angstroms resolution</source><x>, </x><object-id pub-id-type="art-access-id">6AT1</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb6AT1/pdb">http://dx.doi.org/10.2210/pdb6AT1/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3R9J/pdb" source-id-type="uri" id="dataro170"><collab collab-type="author">Lovell S</collab>, <collab collab-type="author">Battaile K.P</collab>, <collab collab-type="author">Park K.-T</collab>, <collab collab-type="author">Wu W</collab>, <collab collab-type="author">Holyoak T</collab>, <collab collab-type="author">Lutkenhaus J</collab>, <year>2011</year><x>, </x><source>4.3A resolution structure of a MinD-MinE(I24N) protein complex</source><x>, </x><object-id pub-id-type="art-access-id">3R9J</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3R9J/pdb">http://dx.doi.org/10.2210/pdb3R9J/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3ABR/pdb" source-id-type="uri" id="dataro171"><collab collab-type="author">Shibata N</collab>, <year>2009</year><x>, </x><source>Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-Cbl (substrate-free form)</source><x>, </x><object-id pub-id-type="art-access-id">3ABR</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3ABR/pdb">http://dx.doi.org/10.2210/pdb3ABR/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3ABS/pdb" source-id-type="uri" id="dataro172"><collab collab-type="author">Shibata N</collab>, <year>2009</year><x>, </x><source>Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with adeninylpentylcobalamin and ethanolamine</source><x>, </x><object-id pub-id-type="art-access-id">3ABS</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3ABS/pdb">http://dx.doi.org/10.2210/pdb3ABS/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb4GD1/pdb" source-id-type="uri" id="dataro173"><collab collab-type="author">Dunkle J.A</collab>, <collab collab-type="author">Wang L</collab>, <collab collab-type="author">Feldman M.B</collab>, <collab collab-type="author">Pulk A</collab>, <collab collab-type="author">Chen V.B</collab>, <collab collab-type="author">Kapral G.J</collab>, <collab collab-type="author">Noeske J</collab>, <collab collab-type="author">Richardson J.S</collab>, <collab collab-type="author">Blanchard S.C</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2012</year><x>, </x><source>Structures of the bacterial ribosome in classical and hybrid states of tRNA binding</source><x>, </x><object-id pub-id-type="art-access-id">4GD1</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb4GD1/pdb">http://dx.doi.org/10.2210/pdb4GD1/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1PCQ/pdb" source-id-type="uri" id="dataro174"><collab collab-type="author">Chaudhry C</collab>, <collab collab-type="author">Farr G.W</collab>, <collab collab-type="author">Todd M.J</collab>, <collab collab-type="author">Rye H.S</collab>, <collab collab-type="author">Brunger A.T</collab>, <collab collab-type="author">Adams P.D</collab>, <collab collab-type="author">Horwich A.L</collab>, <collab collab-type="author">Sigler P.B</collab>, <year>2003</year><x>, </x><source>Crystal structure of groEL-groES</source><x>, </x><object-id pub-id-type="art-access-id">1PCQ</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1PCQ/pdb">http://dx.doi.org/10.2210/pdb1PCQ/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2ACZ/pdb" source-id-type="uri" id="dataro175"><collab collab-type="author">Horsefield R</collab>, <collab collab-type="author">Yankovskaya V</collab>, <collab collab-type="author">Sexton G</collab>, <collab collab-type="author">Whittingham W</collab>, <collab collab-type="author">Shiomi K</collab>, <collab collab-type="author">Omura S</collab>, <collab collab-type="author">Byrne B</collab>, <collab collab-type="author">Cecchini G</collab>, <collab collab-type="author">Iwata S</collab>, <year>2005</year><x>, </x><source>Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 inhibitor co-crystallized at the ubiquinone binding site</source><x>, </x><object-id pub-id-type="art-access-id">2ACZ</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2ACZ/pdb">http://dx.doi.org/10.2210/pdb2ACZ/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1EAY/pdb" source-id-type="uri" id="dataro176"><collab collab-type="author">Mcevoy M.M</collab>, <collab collab-type="author">Hausrath A.C</collab>, <collab collab-type="author">Randolph G.B</collab>, <collab collab-type="author">Remington S.J</collab>, <collab collab-type="author">Dahlquist F.W</collab>, <year>1998</year><x>, </x><source>CHEY-BINDING (P2) DOMAIN OF CHEA IN COMPLEX WITH CHEY FROM ESCHERICHIA COLI</source><x>, </x><object-id pub-id-type="art-access-id">1EAY</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1EAY/pdb">http://dx.doi.org/10.2210/pdb1EAY/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1Y5L/pdb" source-id-type="uri" id="dataro177"><collab collab-type="author">Bertero M.G</collab>, <collab collab-type="author">Rothery R.A</collab>, <collab collab-type="author">Boroumand N</collab>, <collab collab-type="author">Palak M</collab>, <collab collab-type="author">Blasco F</collab>, <collab collab-type="author">Ginet N</collab>, <collab collab-type="author">Weiner J.H</collab>, <collab collab-type="author">Strynadka N.C.J</collab>, <year>2004</year><x>, </x><source>The crystal structure of the NarGHI mutant NarI-H66Y</source><x>, </x><object-id pub-id-type="art-access-id">1Y5L</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1Y5L/pdb">http://dx.doi.org/10.2210/pdb1Y5L/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2QOX/pdb" source-id-type="uri" id="dataro178"><collab collab-type="author">Borovinskaya M.A</collab>, <collab collab-type="author">Shoji S</collab>, <collab collab-type="author">Holton J.M</collab>, <collab collab-type="author">Fredrick K</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with spectinomycin. This file contains the 50S subunit of the second 70S ribosome. The entire crystal structure contains two 70S ribosomes</source><x>, </x><object-id pub-id-type="art-access-id">2QOX</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2QOX/pdb">http://dx.doi.org/10.2210/pdb2QOX/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1FMA/pdb" source-id-type="uri" id="dataro179"><collab collab-type="author">Rudolph M.J</collab>, <collab collab-type="author">Wuebbens M.M</collab>, <collab collab-type="author">Rajagolpalan K.V</collab>, <collab collab-type="author">Schindelin H</collab>, <year>2000</year><x>, </x><source>MOLYBDOPTERIN SYNTHASE (MOAD/MOAE)</source><x>, </x><object-id pub-id-type="art-access-id">1FMA</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1FMA/pdb">http://dx.doi.org/10.2210/pdb1FMA/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3ABO/pdb" source-id-type="uri" id="dataro180"><collab collab-type="author">Shibata N</collab>, <year>2009</year><x>, </x><source>Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-Cbl and ethanolamine</source><x>, </x><object-id pub-id-type="art-access-id">3ABO</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3ABO/pdb">http://dx.doi.org/10.2210/pdb3ABO/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1ACM/pdb" source-id-type="uri" id="dataro181"><collab collab-type="author">Stevens R.C</collab>, <collab collab-type="author">Kantrowitz E.R</collab>, <collab collab-type="author">Lipscomb W.N</collab>, <year>1992</year><x>, </x><source>ARGININE 54 IN THE ACTIVE SITE OF ESCHERICHIA COLI ASPARTATE TRANSCARBAMOYLASE IS CRITICAL FOR CATALYSIS: A SITE-SPECIFIC MUTAGENESIS, NMR AND X-RAY CRYSTALLOGRAPHY STUDY</source><x>, </x><object-id pub-id-type="art-access-id">1ACM</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1ACM/pdb">http://dx.doi.org/10.2210/pdb1ACM/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2FZC/pdb" source-id-type="uri" id="dataro182"><collab collab-type="author">Heng S</collab>, <collab collab-type="author">Stieglitz K.A</collab>, <collab collab-type="author">Eldo J</collab>, <collab collab-type="author">Xia J</collab>, <collab collab-type="author">Cardia J.P</collab>, <collab collab-type="author">Kantrowitz E.R</collab>, <year>2006</year><x>, </x><source>The Structure of Wild-Type E. Coli Aspartate Transcarbamoylase in Complex with Novel T State Inhibitors at 2.10 Resolution</source><x>, </x><object-id pub-id-type="art-access-id">2FZC</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2FZC/pdb">http://dx.doi.org/10.2210/pdb2FZC/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3N3B/pdb" source-id-type="uri" id="dataro183"><collab collab-type="author">Boal A.K</collab>, <collab collab-type="author">Cotruvo J.A Jnr</collab>, <collab collab-type="author">Stubbe J</collab>, <collab collab-type="author">Rosenzweig A.C</collab>, <year>2010</year><x>, </x><source>Ribonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli in Complex with Reduced NrdI with a Trapped Peroxide</source><x>, </x><object-id pub-id-type="art-access-id">3N3B</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3N3B/pdb">http://dx.doi.org/10.2210/pdb3N3B/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3EUH/pdb" source-id-type="uri" id="dataro184"><collab collab-type="author">Suh M.K</collab>, <collab collab-type="author">Ku B</collab>, <collab collab-type="author">Ha N.C</collab>, <collab collab-type="author">Woo J.S</collab>, <collab collab-type="author">Oh B.H</collab>, <year>2008</year><x>, </x><source>Crystal Structure of the MukE-MukF Complex</source><x>, </x><object-id pub-id-type="art-access-id">3EUH</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3EUH/pdb">http://dx.doi.org/10.2210/pdb3EUH/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2QOV/pdb" source-id-type="uri" id="dataro185"><collab collab-type="author">Borovinskaya M.A</collab>, <collab collab-type="author">Shoji S</collab>, <collab collab-type="author">Holton J.M</collab>, <collab collab-type="author">Fredrick K</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with spectinomycin. 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This file contains the 30S subunit of the second 70S ribosome</source><x>, </x><object-id pub-id-type="art-access-id">3ORA</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3ORA/pdb">http://dx.doi.org/10.2210/pdb3ORA/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2HQS/pdb" source-id-type="uri" id="dataro200"><collab collab-type="author">Grishkovskaya I</collab>, <collab collab-type="author">Bonsor D.A</collab>, <collab collab-type="author">Kleanthous C</collab>, <collab collab-type="author">Dodson E.J</collab>, <year>2006</year><x>, </x><source>Crystal structure of TolB/Pal complex</source><x>, </x><object-id pub-id-type="art-access-id">2HQS</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2HQS/pdb">http://dx.doi.org/10.2210/pdb2HQS/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3ABQ/pdb" source-id-type="uri" id="dataro201"><collab collab-type="author">Shibata N</collab>, <year>2009</year><x>, </x><source>Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-Cbl and 2-amino-1-propanol</source><x>, </x><object-id pub-id-type="art-access-id">3ABQ</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3ABQ/pdb">http://dx.doi.org/10.2210/pdb3ABQ/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2B3T/pdb" source-id-type="uri" id="dataro202"><collab collab-type="author">Graille M</collab>, <collab collab-type="author">Heurgue-Hamard V</collab>, <collab collab-type="author">Champ S</collab>, <collab collab-type="author">Mora L</collab>, <collab collab-type="author">Scrima N</collab>, <collab collab-type="author">Ulryck N</collab>, <collab collab-type="author">van Tilbeurgh H</collab>, <collab collab-type="author">Buckingham R.H</collab>, <year>2005</year><x>, </x><source>Molecular basis for bacterial class 1 release factor methylation by PrmC</source><x>, </x><object-id pub-id-type="art-access-id">2B3T</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2B3T/pdb">http://dx.doi.org/10.2210/pdb2B3T/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3M4W/pdb" source-id-type="uri" id="dataro203"><collab collab-type="author">Kim D.Y</collab>, <collab collab-type="author">Kwon E</collab>, <collab collab-type="author">Choi J.K</collab>, <collab collab-type="author">Hwang H.-Y</collab>, <collab collab-type="author">Kim K.K</collab>, <year>2010</year><x>, </x><source>Structural basis for the negative regulation of bacterial stress response by RseB</source><x>, </x><object-id pub-id-type="art-access-id">3M4W</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3M4W/pdb">http://dx.doi.org/10.2210/pdb3M4W/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3I1R/pdb" source-id-type="uri" id="dataro204"><collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Dunkle J.A</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2009</year><x>, </x><source>Crystal structure of the E. coli 70S ribosome in an intermediate state of ratcheting</source><x>, </x><object-id pub-id-type="art-access-id">3I1R</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3I1R/pdb">http://dx.doi.org/10.2210/pdb3I1R/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2QAO/pdb" source-id-type="uri" id="dataro205"><collab collab-type="author">Borovinskaya M.A</collab>, <collab collab-type="author">Pai R.D</collab>, <collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Schuwirth B.-S</collab>, <collab collab-type="author">Holton J.M</collab>, <collab collab-type="author">Hirokawa G</collab>, <collab collab-type="author">Kaji H</collab>, <collab collab-type="author">Kaji A</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with neomycin. This file contains the 50S subunit of the second 70S ribosome, with neomycin bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400</source><x>, </x><object-id pub-id-type="art-access-id">2QAO</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2QAO/pdb">http://dx.doi.org/10.2210/pdb2QAO/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1C3O/pdb" source-id-type="uri" id="dataro206"><collab collab-type="author">Thoden J.B</collab>, <collab collab-type="author">Huang X</collab>, <collab collab-type="author">Raushel F.M</collab>, <collab collab-type="author">Holden H.M</collab>, <year>1999</year><x>, </x><source>CRYSTAL STRUCTURE OF THE CARBAMOYL PHOSPHATE SYNTHETASE: SMALL SUBUNIT MUTANT C269S WITH BOUND GLUTAMINE</source><x>, </x><object-id pub-id-type="art-access-id">1C3O</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1C3O/pdb">http://dx.doi.org/10.2210/pdb1C3O/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3CIR/pdb" source-id-type="uri" id="dataro207"><collab collab-type="author">Tomasiak T.M</collab>, <collab collab-type="author">Maklashina E</collab>, <collab collab-type="author">Cecchini G</collab>, <collab collab-type="author">Iverson T.M</collab>, <year>2008</year><x>, </x><source>E. coli Quinol fumarate reductase FrdA T234A mutation</source><x>, </x><object-id pub-id-type="art-access-id">3CIR</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3CIR/pdb">http://dx.doi.org/10.2210/pdb3CIR/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3RLF/pdb" source-id-type="uri" id="dataro208"><collab collab-type="author">Oldham M.L</collab>, <collab collab-type="author">Chen J</collab>, <year>2011</year><x>, </x><source>Crystal structure of the maltose-binding protein/maltose transporter complex in an outward-facing conformation bound to MgAMPPNP</source><x>, </x><object-id pub-id-type="art-access-id">3RLF</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3RLF/pdb">http://dx.doi.org/10.2210/pdb3RLF/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2WU2/pdb" source-id-type="uri" id="dataro209"><collab collab-type="author">Ruprecht J</collab>, <collab collab-type="author">Yankovskaya V</collab>, <collab collab-type="author">Maklashina E</collab>, <collab collab-type="author">Iwata S</collab>, <collab collab-type="author">Cecchini G</collab>, <year>2009</year><x>, </x><source>Crystal structure of the E. coli succinate:quinone oxidoreductase (SQR) SdhC His84Met mutant</source><x>, </x><object-id pub-id-type="art-access-id">2WU2</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2WU2/pdb">http://dx.doi.org/10.2210/pdb2WU2/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb8ATC/pdb" source-id-type="uri" id="dataro210"><collab collab-type="author">Ke H</collab>, <collab collab-type="author">Lipscomb W.N</collab>, <collab collab-type="author">Cho Y</collab>, <collab collab-type="author">Honzatko R.B</collab>, <year>1989</year><x>, </x><source>COMPLEX OF N-PHOSPHONACETYL-L-ASPARTATE WITH ASPARTATE CARBAMOYLTRANSFERASE. 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</x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1Y5N/pdb">http://dx.doi.org/10.2210/pdb1Y5N/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3EUK/pdb" source-id-type="uri" id="dataro212"><collab collab-type="author">Woo J.S</collab>, <collab collab-type="author">Lim J.H</collab>, <collab collab-type="author">Shin H.C</collab>, <collab collab-type="author">Oh B.H</collab>, <year>2008</year><x>, </x><source>Crystal structure of MukE-MukF(residues 292-443)-MukB(head domain)-ATPgammaS complex, asymmetric dimer</source><x>, </x><object-id pub-id-type="art-access-id">3EUK</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3EUK/pdb">http://dx.doi.org/10.2210/pdb3EUK/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3DHW/pdb" source-id-type="uri" id="dataro213"><collab collab-type="author">Rees D.C</collab>, <collab collab-type="author">Kaiser J.T</collab>, <collab collab-type="author">Kadaba N.S</collab>, <collab collab-type="author">Johnson E</collab>, <collab collab-type="author">Lee A.T</collab>, <year>2008</year><x>, </x><source>Crystal structure of methionine importer MetNI</source><x>, </x><object-id pub-id-type="art-access-id">3DHW</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3DHW/pdb">http://dx.doi.org/10.2210/pdb3DHW/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1TTH/pdb" source-id-type="uri" id="dataro214"><collab collab-type="author">Stieglitz K</collab>, <collab collab-type="author">Stec B</collab>, <collab collab-type="author">Baker D.P</collab>, <collab collab-type="author">Kantrowitz E.R</collab>, <year>2004</year><x>, </x><source>Aspartate Transcarbamoylase Catalytic Chain Mutant Glu50Ala Complexed with N-(Phosphonacetyl-L-Aspartate) (PALA)</source><x>, </x><object-id pub-id-type="art-access-id">1TTH</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1TTH/pdb">http://dx.doi.org/10.2210/pdb1TTH/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1XJW/pdb" source-id-type="uri" id="dataro215"><collab collab-type="author">Stieglitz K.A</collab>, <collab collab-type="author">Alam N</collab>, <collab collab-type="author">Xia J</collab>, <collab collab-type="author">Gourinath S</collab>, <collab collab-type="author">Tsuruta H</collab>, <collab collab-type="author">Kantrowitz E.R</collab>, <year>2004</year><x>, </x><source>The Structure of E. coli Aspartate Transcarbamoylase Q137A Mutant in The R-State</source><x>, </x><object-id pub-id-type="art-access-id">1XJW</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1XJW/pdb">http://dx.doi.org/10.2210/pdb1XJW/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1MBX/pdb" source-id-type="uri" id="dataro216"><collab collab-type="author">Guo F</collab>, <collab collab-type="author">Esser L</collab>, <collab collab-type="author">Singh S.K</collab>, <collab collab-type="author">Maurizi M.R</collab>, <collab collab-type="author">Xia D</collab>, <year>2002</year><x>, </x><source>CRYSTAL STRUCTURE ANALYSIS OF ClpSN WITH TRANSITION METAL ION BOUND</source><x>, </x><object-id pub-id-type="art-access-id">1MBX</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1MBX/pdb">http://dx.doi.org/10.2210/pdb1MBX/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3MPU/pdb" source-id-type="uri" id="dataro217"><collab collab-type="author">Mendes K.R</collab>, <collab collab-type="author">Kantrowitz E.R</collab>, <year>2010</year><x>, </x><source>Crystal structure of the C47A/A241C disulfide-linked E. coli Aspartate Transcarbamoylase holoenzyme</source><x>, </x><object-id pub-id-type="art-access-id">3MPU</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3MPU/pdb">http://dx.doi.org/10.2210/pdb3MPU/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1EZZ/pdb" source-id-type="uri" id="dataro218"><collab collab-type="author">Jin L</collab>, <collab collab-type="author">Stec B</collab>, <collab collab-type="author">Kantrowitz E.R</collab>, <year>2000</year><x>, </x><source>CRYSTAL STRUCTURE OF E. COLI ASPARTATE TRANSCARBAMOYLASE P268A MUTANT IN THE T-STATE</source><x>, </x><object-id pub-id-type="art-access-id">1EZZ</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1EZZ/pdb">http://dx.doi.org/10.2210/pdb1EZZ/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3OAT/pdb" source-id-type="uri" id="dataro219"><collab collab-type="author">Dunkle J.A</collab>, <collab collab-type="author">Xiong L</collab>, <collab collab-type="author">Mankin A.S</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2010</year><x>, </x><source>Crystal structure of the E. coli ribosome bound to telithromycin. This file contains the 50S subunit of the first 70S ribosome with telithromycin bound</source><x>, </x><object-id pub-id-type="art-access-id">3OAT</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3OAT/pdb">http://dx.doi.org/10.2210/pdb3OAT/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3HI2/pdb" source-id-type="uri" id="dataro220"><collab collab-type="author">Grigoriu S</collab>, <collab collab-type="author">Brown B.L</collab>, <collab collab-type="author">Arruda J.M</collab>, <collab collab-type="author">Peti W</collab>, <collab collab-type="author">Page R</collab>, <year>2009</year><x>, </x><source>Structure of the N-terminal domain of the E. coli antitoxin MqsA (YgiT/b3021) in complex with the E. coli toxin MqsR (YgiU/b3022)</source><x>, </x><object-id pub-id-type="art-access-id">3HI2</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3HI2/pdb">http://dx.doi.org/10.2210/pdb3HI2/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1MBU/pdb" source-id-type="uri" id="dataro221"><collab collab-type="author">Guo F</collab>, <collab collab-type="author">Esser L</collab>, <collab collab-type="author">Singh S.K</collab>, <collab collab-type="author">Maurizi M.R</collab>, <collab collab-type="author">Xia D</collab>, <year>2002</year><x>, </x><source>Crystal Structure Analysis of ClpSN heterodimer</source><x>, </x><object-id pub-id-type="art-access-id">1MBU</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1MBU/pdb">http://dx.doi.org/10.2210/pdb1MBU/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1MBV/pdb" source-id-type="uri" id="dataro222"><collab collab-type="author">Guo F</collab>, <collab collab-type="author">Esser L</collab>, <collab collab-type="author">Singh S.K</collab>, <collab collab-type="author">Maurizi M.R</collab>, <collab collab-type="author">Xia D</collab>, <year>2002</year><x>, </x><source>CRYSTAL STRUCTURE ANALYSIS OF ClpSN HETERODIMER TETRAGONAL FORM</source><x>, </x><object-id pub-id-type="art-access-id">1MBV</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1MBV/pdb">http://dx.doi.org/10.2210/pdb1MBV/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3OAQ/pdb" source-id-type="uri" id="dataro223"><collab collab-type="author">Dunkle J.A</collab>, <collab collab-type="author">Xiong L</collab>, <collab collab-type="author">Mankin A.S</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2010</year><x>, </x><source>Crystal structure of the E. coli ribosome bound to telithromycin. 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</x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2QI9/pdb">http://dx.doi.org/10.2210/pdb2QI9/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1Y5I/pdb" source-id-type="uri" id="dataro232"><collab collab-type="author">Bertero M.G</collab>, <collab collab-type="author">Rothery R.A</collab>, <collab collab-type="author">Boroumand N</collab>, <collab collab-type="author">Palak M</collab>, <collab collab-type="author">Blasco F</collab>, <collab collab-type="author">Ginet N</collab>, <collab collab-type="author">Weiner J.H</collab>, <collab collab-type="author">Strynadka N.C.J</collab>, <year>2004</year><x>, </x><source>The crystal structure of the NarGHI mutant NarI-K86A</source><x>, </x><object-id pub-id-type="art-access-id">1Y5I</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1Y5I/pdb">http://dx.doi.org/10.2210/pdb1Y5I/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3OFO/pdb" source-id-type="uri" id="dataro233"><collab collab-type="author">Dunkle J.A</collab>, <collab collab-type="author">Xiong L</collab>, <collab collab-type="author">Mankin A.S</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2010</year><x>, </x><source>Crystal structure of the E. coli ribosome bound to erythromycin. 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This file contains the 50S subunit of the second 70S ribosome</source><x>, </x><object-id pub-id-type="art-access-id">3OAS</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3OAS/pdb">http://dx.doi.org/10.2210/pdb3OAS/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3PNL/pdb" source-id-type="uri" id="dataro240"><collab collab-type="author">Shi R</collab>, <collab collab-type="author">McDonald L</collab>, <collab collab-type="author">Matte A</collab>, <collab collab-type="author">Cygler M</collab>, <collab collab-type="author">Ekiel I</collab>, , <collab>Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)</collab><year>2010</year><x>, </x><source>Crystal Structure of E.coli Dha kinase DhaK-DhaL complex</source><x>, </x><object-id pub-id-type="art-access-id">3PNL</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3PNL/pdb">http://dx.doi.org/10.2210/pdb3PNL/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2QP1/pdb" source-id-type="uri" id="dataro241"><collab collab-type="author">Borovinskaya M.A</collab>, <collab collab-type="author">Shoji S</collab>, <collab collab-type="author">Holton J.M</collab>, <collab collab-type="author">Fredrick K</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with spectinomycin and neomycin. This file contains the 50S subunit of the second 70S ribosome, with neomycin bound. The entire crystal structure contains two 70S ribosomes</source><x>, </x><object-id pub-id-type="art-access-id">2QP1</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2QP1/pdb">http://dx.doi.org/10.2210/pdb2QP1/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3OAR/pdb" source-id-type="uri" id="dataro242"><collab collab-type="author">Dunkle J.A</collab>, <collab collab-type="author">Xiong L</collab>, <collab collab-type="author">Mankin A.S</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2010</year><x>, </x><source>Crystal structure of the E. coli ribosome bound to telithromycin. This file contains the 30S subunit of the second 70S ribosome</source><x>, </x><object-id pub-id-type="art-access-id">3OAR</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3OAR/pdb">http://dx.doi.org/10.2210/pdb3OAR/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2QBE/pdb" source-id-type="uri" id="dataro243"><collab collab-type="author">Borovinskaya M.A</collab>, <collab collab-type="author">Pai R.D</collab>, <collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Schuwirth B.-S</collab>, <collab collab-type="author">Holton J.M</collab>, <collab collab-type="author">Hirokawa G</collab>, <collab collab-type="author">Kaji H</collab>, <collab collab-type="author">Kaji A</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with ribosome recycling factor (RRF). This file contains the 50S subunit of the first 70S ribosome, with RRF bound. The entire crystal structure contains two 70S ribosomes and is described in remark 400</source><x>, </x><object-id pub-id-type="art-access-id">2QBE</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2QBE/pdb">http://dx.doi.org/10.2210/pdb2QBE/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1RAB/pdb" source-id-type="uri" id="dataro244"><collab collab-type="author">Kosman R.P</collab>, <collab collab-type="author">Gouaux J.E</collab>, <collab collab-type="author">Lipscomb W.N</collab>, <year>1992</year><x>, </x><source>CRYSTAL STRUCTURE OF CTP-LIGATED T STATE ASPARTATE TRANSCARBAMOYLASE AT 2.5 ANGSTROMS RESOLUTION: IMPLICATIONS FOR ATCASE MUTANTS AND THE MECHANISM OF NEGATIVE COOPERATIVITY</source><x>, </x><object-id pub-id-type="art-access-id">1RAB</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1RAB/pdb">http://dx.doi.org/10.2210/pdb1RAB/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1RAC/pdb" source-id-type="uri" id="dataro245"><collab collab-type="author">Kosman R.P</collab>, <collab collab-type="author">Gouaux J.E</collab>, <collab collab-type="author">Lipscomb W.N</collab>, <year>1992</year><x>, </x><source>CRYSTAL STRUCTURE OF CTP-LIGATED T STATE ASPARTATE TRANSCARBAMOYLASE AT 2.5 ANGSTROMS RESOLUTION: IMPLICATIONS FOR ATCASE MUTANTS AND THE MECHANISM OF NEGATIVE COOPERATIVITY</source><x>, </x><object-id pub-id-type="art-access-id">1RAC</object-id><x>; 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</x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1RAF/pdb">http://dx.doi.org/10.2210/pdb1RAF/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1RAG/pdb" source-id-type="uri" id="dataro248"><collab collab-type="author">Kosman R.P</collab>, <collab collab-type="author">Gouaux J.E</collab>, <collab collab-type="author">Lipscomb W.N</collab>, <year>1992</year><x>, </x><source>CRYSTAL STRUCTURE OF CTP-LIGATED T STATE ASPARTATE TRANSCARBAMOYLASE AT 2.5 ANGSTROMS RESOLUTION: IMPLICATIONS FOR ATCASE MUTANTS AND THE MECHANISM OF NEGATIVE COOPERATIVITY</source><x>, </x><object-id pub-id-type="art-access-id">1RAG</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1RAG/pdb">http://dx.doi.org/10.2210/pdb1RAG/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1RAD/pdb" source-id-type="uri" id="dataro249"><collab collab-type="author">Kosman R.P</collab>, <collab collab-type="author">Gouaux J.E</collab>, <collab collab-type="author">Lipscomb W.N</collab>, <year>1992</year><x>, </x><source>CRYSTAL STRUCTURE OF CTP-LIGATED T STATE ASPARTATE TRANSCARBAMOYLASE AT 2.5 ANGSTROMS RESOLUTION: IMPLICATIONS FOR ATCASE MUTANTS AND THE MECHANISM OF NEGATIVE COOPERATIVITY</source><x>, </x><object-id pub-id-type="art-access-id">1RAD</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1RAD/pdb">http://dx.doi.org/10.2210/pdb1RAD/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1RAE/pdb" source-id-type="uri" id="dataro250"><collab collab-type="author">Kosman R.P</collab>, <collab collab-type="author">Gouaux J.E</collab>, <collab collab-type="author">Lipscomb W.N</collab>, <year>1992</year><x>, </x><source>CRYSTAL STRUCTURE OF CTP-LIGATED T STATE ASPARTATE TRANSCARBAMOYLASE AT 2.5 ANGSTROMS RESOLUTION: IMPLICATIONS FOR ATCASE MUTANTS AND THE MECHANISM OF NEGATIVE COOPERATIVITY</source><x>, </x><object-id pub-id-type="art-access-id">1RAE</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1RAE/pdb">http://dx.doi.org/10.2210/pdb1RAE/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1KQG/pdb" source-id-type="uri" id="dataro251"><collab collab-type="author">Jormakka M</collab>, <collab collab-type="author">Tornroth S</collab>, <collab collab-type="author">Byrne B</collab>, <collab collab-type="author">Iwata S</collab>, <year>2002</year><x>, </x><source>FORMATE DEHYDROGENASE N FROM E. COLI</source><x>, </x><object-id pub-id-type="art-access-id">1KQG</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1KQG/pdb">http://dx.doi.org/10.2210/pdb1KQG/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1KQF/pdb" source-id-type="uri" id="dataro252"><collab collab-type="author">Jormakka M</collab>, <collab collab-type="author">Tornroth S</collab>, <collab collab-type="author">Byrne B</collab>, <collab collab-type="author">Iwata S</collab>, <year>2002</year><x>, </x><source>FORMATE DEHYDROGENASE N FROM E. COLI</source><x>, </x><object-id pub-id-type="art-access-id">1KQF</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1KQF/pdb">http://dx.doi.org/10.2210/pdb1KQF/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1RAH/pdb" source-id-type="uri" id="dataro253"><collab collab-type="author">Kosman R.P</collab>, <collab collab-type="author">Gouaux J.E</collab>, <collab collab-type="author">Lipscomb W.N</collab>, <year>1992</year><x>, </x><source>CRYSTAL STRUCTURE OF CTP-LIGATED T STATE ASPARTATE TRANSCARBAMOYLASE AT 2.5 ANGSTROMS RESOLUTION: IMPLICATIONS FOR ATCASE MUTANTS AND THE MECHANISM OF NEGATIVE COOPERATIVITY</source><x>, </x><object-id pub-id-type="art-access-id">1RAH</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1RAH/pdb">http://dx.doi.org/10.2210/pdb1RAH/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1RAI/pdb" source-id-type="uri" id="dataro254"><collab collab-type="author">Kosman R.P</collab>, <collab collab-type="author">Gouaux J.E</collab>, <collab collab-type="author">Lipscomb W.N</collab>, <year>1992</year><x>, </x><source>CRYSTAL STRUCTURE OF CTP-LIGATED T STATE ASPARTATE TRANSCARBAMOYLASE AT 2.5 ANGSTROMS RESOLUTION: IMPLICATIONS FOR ATCASE MUTANTS AND THE MECHANISM OF NEGATIVE COOPERATIVITY</source><x>, </x><object-id pub-id-type="art-access-id">1RAI</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1RAI/pdb">http://dx.doi.org/10.2210/pdb1RAI/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb8AT1/pdb" source-id-type="uri" id="dataro255"><collab collab-type="author">Gouaux J.E</collab>, <collab collab-type="author">Stevens R.C</collab>, <collab collab-type="author">Lipscomb W.N</collab>, <year>1989</year><x>, </x><source>CRYSTAL STRUCTURES OF ASPARTATE CARBAMOYLTRANSFERASE LIGATED WITH PHOSPHONOACETAMIDE, MALONATE, AND CTP OR ATP AT 2.8-ANGSTROMS RESOLUTION AND NEUTRAL P*H</source><x>, </x><object-id pub-id-type="art-access-id">8AT1</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb8AT1/pdb">http://dx.doi.org/10.2210/pdb8AT1/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1SVT/pdb" source-id-type="uri" id="dataro256"><collab collab-type="author">Chaudhry C</collab>, <collab collab-type="author">Horwich A.L</collab>, <collab collab-type="author">Brunger A.T</collab>, <collab collab-type="author">Adams P.D</collab>, <year>2004</year><x>, </x><source>Crystal structure of GroEL14-GroES7-(ADP-AlFx)7</source><x>, </x><object-id pub-id-type="art-access-id">1SVT</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1SVT/pdb">http://dx.doi.org/10.2210/pdb1SVT/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3PV0/pdb" source-id-type="uri" id="dataro257"><collab collab-type="author">Oldham M.L</collab>, <collab collab-type="author">Chen J</collab>, <year>2010</year><x>, </x><source>Crystal Structure of a pre-translocation state MBP-Maltose transporter complex without nucleotide</source><x>, </x><object-id pub-id-type="art-access-id">3PV0</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3PV0/pdb">http://dx.doi.org/10.2210/pdb3PV0/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1R6O/pdb" source-id-type="uri" id="dataro258"><collab collab-type="author">Xia D</collab>, <collab collab-type="author">Maurizi M.R</collab>, <collab collab-type="author">Guo F</collab>, <collab collab-type="author">Singh S.K</collab>, <collab collab-type="author">Esser L</collab>, <year>2003</year><x>, </x><source>ATP-dependent Clp protease ATP-binding subunit clpA/ATP-dependent Clp protease adaptor protein clpS</source><x>, </x><object-id pub-id-type="art-access-id">1R6O</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1R6O/pdb">http://dx.doi.org/10.2210/pdb1R6O/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3UOS/pdb" source-id-type="uri" id="dataro259"><collab collab-type="author">Zhou J</collab>, <collab collab-type="author">Lancaster L</collab>, <collab collab-type="author">Trakhanov S</collab>, <collab collab-type="author">Noller H.F</collab>, <year>2011</year><x>, </x><source>Crystal Structure of Release Factor RF3 Trapped in the GTP State on a Rotated Conformation of the Ribosome (without viomycin)</source><x>, </x><object-id pub-id-type="art-access-id">3UOS</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3UOS/pdb">http://dx.doi.org/10.2210/pdb3UOS/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1W36/pdb" source-id-type="uri" id="dataro260"><collab collab-type="author">Singleton M.R</collab>, <collab collab-type="author">Dillingham M.S</collab>, <collab collab-type="author">Gaudier M</collab>, <collab collab-type="author">Kowalczykowski S.C</collab>, <collab collab-type="author">Wigley D.B</collab>, <year>2004</year><x>, </x><source>RecBCD: DNA complex</source><x>, </x><object-id pub-id-type="art-access-id">1W36</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1W36/pdb">http://dx.doi.org/10.2210/pdb1W36/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2QBD/pdb" source-id-type="uri" id="dataro261"><collab collab-type="author">Borovinskaya M.A</collab>, <collab collab-type="author">Pai R.D</collab>, <collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Schuwirth BS</collab>, <collab collab-type="author">Holton J.M</collab>, <collab collab-type="author">Hirokawa G</collab>, <collab collab-type="author">Kaji H</collab>, <collab collab-type="author">Kaji A</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with ribosome recycling factor (RRF). This file contains the 30S subunit of the first 70S ribosome. The entire crystal structure contains two 70S ribosomes and is described in remark 400</source><x>, </x><object-id pub-id-type="art-access-id">2QBD</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2QBD/pdb">http://dx.doi.org/10.2210/pdb2QBD/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3AT1/pdb" source-id-type="uri" id="dataro262"><collab collab-type="author">Gouaux J.E</collab>, <collab collab-type="author">Lipscomb W.N</collab>, <year>1989</year><x>, </x><source>CRYSTAL STRUCTURES OF PHOSPHONOACETAMIDE LIGATED T AND PHOSPHONOACETAMIDE AND MALONATE LIGATED R STATES OF ASPARTATE CARBAMOYLTRANSFERASE AT 2.8-ANGSTROMS RESOLUTION AND NEUTRAL PH</source><x>, </x><object-id pub-id-type="art-access-id">3AT1</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3AT1/pdb">http://dx.doi.org/10.2210/pdb3AT1/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb3VTI/pdb" source-id-type="uri" id="dataro263"><collab collab-type="author">Shomura Y</collab>, <collab collab-type="author">Higuchi Y</collab>, <year>2012</year><x>, </x><source>Crystal structure of HypE-HypF complex</source><x>, </x><object-id pub-id-type="art-access-id">3VTI</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb3VTI/pdb">http://dx.doi.org/10.2210/pdb3VTI/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1LZW/pdb" source-id-type="uri" id="dataro264"><collab collab-type="author">Zeth K</collab>, <collab collab-type="author">Ravelli R.B</collab>, <collab collab-type="author">Paal K</collab>, <collab collab-type="author">Cusack S</collab>, <collab collab-type="author">Bukau B</collab>, <collab collab-type="author">Dougan D.A</collab>, <year>2002</year><x>, </x><source>Structural basis of ClpS-mediated switch in ClpA substrate recognition</source><x>, </x><object-id pub-id-type="art-access-id">1LZW</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1LZW/pdb">http://dx.doi.org/10.2210/pdb1LZW/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2I2T/pdb" source-id-type="uri" id="dataro265"><collab collab-type="author">Berk V</collab>, <collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Pai R.D</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2006</year><x>, </x><source>Crystal Structure of Ribosome with messenger RNA and the Anticodon stem-loop of P-site tRNA. This file contains the 50s subunit of one 70s ribosome. The entire crystal structure contains two 70s ribosomes and is described in remark 400</source><x>, </x><object-id pub-id-type="art-access-id">2I2T</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2I2T/pdb">http://dx.doi.org/10.2210/pdb2I2T/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2QOY/pdb" source-id-type="uri" id="dataro266"><collab collab-type="author">Borovinskaya M.A</collab>, <collab collab-type="author">Shoji S</collab>, <collab collab-type="author">Holton J.M</collab>, <collab collab-type="author">Fredrick K</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with spectinomycin and neomycin. This file contains the 30S subunit of the first 70S ribosome, with spectinomycin and neomycin bound. The entire crystal structure contains two 70S ribosomes</source><x>, </x><object-id pub-id-type="art-access-id">2QOY</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb2QOY/pdb">http://dx.doi.org/10.2210/pdb2QOY/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb1ZA2/pdb" source-id-type="uri" id="dataro267"><collab collab-type="author">Wang J</collab>, <collab collab-type="author">Stieglitz K.A</collab>, <collab collab-type="author">Cardia J.P</collab>, <collab collab-type="author">Kantrowitz E.R</collab>, <year>2005</year><x>, </x><source>Structure of wild-type E. coli Aspartate Transcarbamoylase in the presence of CTP, carbamoyl phosphate at 2.50 A resolution</source><x>, </x><object-id pub-id-type="art-access-id">1ZA2</object-id><x>; </x><ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.2210/pdb1ZA2/pdb">http://dx.doi.org/10.2210/pdb1ZA2/pdb</ext-link><x>, </x><comment>Publicly available at the RCSB Protein Data Bank.</comment></related-object></p><p><related-object content-type="existing-dataset" source-id="http://dx.doi.org/10.2210/pdb2QBG/pdb" source-id-type="uri" id="dataro268"><collab collab-type="author">Borovinskaya M.A</collab>, <collab collab-type="author">Pai R.D</collab>, <collab collab-type="author">Zhang W</collab>, <collab collab-type="author">Schuwirth BS</collab>, <collab collab-type="author">Holton JM</collab>, <collab collab-type="author">Hirokawa G</collab>, <collab collab-type="author">Kaji H</collab>, <collab collab-type="author">Kaji A</collab>, <collab collab-type="author">Cate J.H.D</collab>, <year>2007</year><x>, </x><source>Crystal structure of the bacterial ribosome from Escherichia coli in complex with ribosome recycling factor (RRF). This file contains the 50S subunit of the second 70S ribosome, with RRF bound. 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An edited version of the letter sent to the authors after peer review is shown, indicating the substantive concerns or comments; minor concerns are not usually shown. Reviewers have the opportunity to discuss the decision before the letter is sent (see <ext-link ext-link-type="uri" xlink:href="http://elifesciences.org/review-process">review process</ext-link>). Similarly, the author response typically shows only responses to the major concerns raised by the reviewers.</p></boxed-text><p>Thank you for sending your work entitled “Sequence co-evolution gives 3D contacts and structures of protein complexes”““ for consideration at <italic>eLife.</italic> Your article has been favorably evaluated by John Kuriyan (Senior editor), working with a member of our Board of Reviewing Editors, and 3 reviewers.</p><p>The editors and the other reviewers discussed their comments before we reached this decision, and the Reviewing editor has assembled the following comments to help you prepare a revised submission.</p><p>This manuscript describes an approach to predict 3D residue-residue contacts at protein interfaces from an analysis of multiple sequence alignments. The described computational approach (using sequence co-evolution to predict contacts between interacting proteins and to generate three-dimensional models of complex structures) appears to be quite successful and is an important contribution that is of interest to a broad audience. The analyses, results, and conclusions are similar to work conducted during the same period by Baker & coworkers, published recently in <italic>eLife.</italic> Nevertheless, it is the consensus opinion of the reviewers that the present manuscript is potentially suitable for publication in <italic>eLife</italic> as well, provided that all of the comments raised by the reviewers can be addressed satisfactorily.</p><p>We have appended the comments from the three reviewers below. Although many individual points are raised, you will see that the principal concern of the reviewers is that the manuscript falls short of providing the reader with sufficient analysis to judge the validity of the conclusions. It should be possible for you to revise the manuscript to address these concerns without much in the way of new calculations, so we hope that it should be relatively straightforward to deal with these issues.</p><p>In addition, since the Baker paper came out recently, it should be given appropriate credit in a revised version. We recommend removing the word “new” from the manuscript for this reason, and instead simply state what was done.</p><p><italic>Reviewer 1:</italic></p><p>1) The Abstract claims that the authors' approach can discriminate between interacting and non-interacting proteins. However, as far as I can see, the rest of the paper concerns only calculating the interface residues of proteins which are known to interact. No evidence is presented to support the claim to be able to calculate non-interactors. The authors' claim should be corrected accordingly.</p><p>2) The authors claim that the co-evolutionary approach has not previously been applied to prediction of protein-protein interfaces. This is incorrect, as the authors seem to be unaware of the previous work of Raphael Guerois' group, which seems rather surprising. The authors should acknowledge the prior work of Faure et al (2012) and Andreani et al. (2013), and they should modify their claim to novelty accordingly. It would also be appropriate to cite properly the prior work of the Baker group (Ovchinnikov et al., 2014) in the same paragraph (the authors currently mention this work only as a “note added during submission”), and the recent review by Andreani and Guerois (2014).</p><p>3) In several places the authors say that their approach exploits the fact that interacting proteins are often coded close to each other in a genome. Why is this assumption necessary? According to the description given in Methods, any pair of sequences which are presumed to interact could be concatenated and then used in the authors method. Please clarify.</p><p>4) If I understand the authors’ method correctly, they first concatenate the multiple sequences of the presumed interactors, and they then use their previous approach for detecting interacting pairs of columns in the multiple alignment. In this case, when concatenating the alignments for protein “A” with those of protein “B”, the “intra-EC” pairs would appear as A-A and B-B pairs, while the “inter-EC” pairs would come from A-B or B-A interactions. My question is then, are there any observable differences in the inter and intra scores? One might expect that the conservation scores would be lower for inter interactions than intra interactions, as an interface might show more “plasticity” than the core of a domain. It would be very interesting if the authors could comment on this, preferably supported by numerical results.</p><p>5) It is incorrect for the authors to refer to their own data set as a “benchmark”. Suggestion: remove all references to the term “benchmark”. However, if the authors make all their data available in a convenient way on-line, it could be proposed as a new “benchmark”.</p><p>6) It is wrong to claim that “Experimental evidence... agrees with EVcomplex predictions” (!). Please rewrite this to say that your predictions agree with the experimental evidence. But, if this is your claim, please also support it in some way. What is the experimental evidence? How to you calculate and quantify “agrees with”?</p><p>7) Same point in the main text. “The resulting model is consistent with the topologies from cross-linking”. How do you quantify consistent? RMSD from the earlier models? Please provide supporting details.</p><p><italic>Reviewer 2:</italic></p><p>My main comments concern the way the data in the current manuscript are analyzed and presented. While the main Figures / <xref ref-type="table" rid="tbl1">Table 1</xref> currently illustrate useful examples, they should also show overall analyses of the results over all cases in the benchmark datasets. In several cases this is essential to support the stated conclusions. It does not seem that this would require a substantial amount of new work or lengthy simulations, as most of the relevant data are in the Supplementary Materials (most data are in raw table format or with a separate Figure for each example, which makes it hard for the reader to gauge overall performance – this could be presented in a more easily digestible format in the main text). Specifically, I feel the paper could be substantially improved if the following points were addressed:</p><p>1) Please support the statement “Benchmark calculations here ... indicate that the number of sequences in the alignment is critical...” with a Figure showing overall performance versus # of sequences (<xref ref-type="fig" rid="fig3">Figure 3</xref> shows dependency of accuracy on relative rank for only two examples).</p><p>2) Show a main Figure comparing predicted contacts against residue distances in the 30 known crystal structures of complexes that had a sufficient number of sequences (<xref ref-type="fig" rid="fig2">Figure 2</xref> only shows contact plots for two examples, and structural pictures for several more, but no overall quantification). This type of analysis could also help to support the statement “For the top ranked benchmark complexes, the majority of the top 5 ECs is correct to within 8A...” with a more quantitative analysis (<xref ref-type="table" rid="tbl1">Table 1</xref> only shows 7 of the 30 complexes in the dataset; <xref ref-type="supplementary-material" rid="SD3-data">Supplementary file 3</xref> shows all individual contact maps, but no overall quantification).</p><p>3) “... these benchmarks show ... and demonstrate the criteria needed for successful prediction of unknown interactions”. To support this statement, it would be useful to have a main Figure / Table for each important criterion, analyzed over an entire benchmark set (as for the number of sequences in point 1).</p><p>4) Please add metrics to support statements that ECs are “completely consistent” with crosslinking data, or that a coupling “coincides with experimental evidence”. The comparison Table in Supplementary Figure 6 could be presented in more quantitative terms in the main text (for example, what does “crosslinking neighborhood” mean?).</p><p>5) What are the possible reasons for false-positive co-variation that does not correspond to contact?</p><p>6) The manuscript deals entirely with pairwise co-evolution, and seems to neglect the possibility of higher-order complexity in the sequence pattern.</p><p><italic>Reviewer 3:</italic></p><p>The manuscript presents an upbeat and optimistic view of the success of the method, with a relatively small amount of critical discussion and little if any investigation of what one can learn from cases in which it does not perform as expected. (For example, a list of possible reasons for false-positive co-variation that does not correspond to contact is given, but an analysis of actual instances is not.) Likewise, a set of methods is presented that is relatively particular, and the reason why these specific methods were chosen over other possibilities is not provided. Moreover, the manuscript deals entirely with pairwise co-evolution, and seems to neglect the possibility of higher-order complexity in the sequence pattern. The manuscript could be substantially strengthened by adding analyses and insights in these issues.</p></body></sub-article><sub-article article-type="reply" id="SA2"><front-stub><article-id pub-id-type="doi">10.7554/eLife.03430.032</article-id><title-group><article-title>Author response</article-title></title-group></front-stub><body><p>Thank you for your comments and forwarded reviews of our paper. The revised paper addresses the questions from the reviewers. As you point out, the principal request of the reviewers was to see more quantitative analysis to judge the validity of the conclusions. This is addressed by detailed additions to the paper including:</p><p>1) A quantitative analysis of the accuracy with summary statistics (<xref ref-type="fig" rid="fig2">Figure 2A,B & C</xref>, with Supplementary figures, tables and data for each individual complex).</p><p>2) The use of the EVcomplex scores for inter-protein ECs that allow comparison across proteins (<xref ref-type="fig" rid="fig2">Figure 2A</xref>, Materials and methods, Supplementary files).</p><p>3) A fuller analysis and clearer explanation of how the scores are used to distinguish interactions from non-interactions with a proof of principle exercise of all ATP synthase subunits against all others (a total of 28 interactions), resulting in 86% accuracy.</p><p>4) Detailed analysis of agreement of cross-linking experiments and predictions for a –subunit ECs and a- to b- subunit inter-ECs, <xref ref-type="supplementary-material" rid="SD6-data">Supplementary file 6</xref> and <xref ref-type="fig" rid="fig7">Author response image 1</xref>.<fig id="fig7" position="float"><label>Author response image 1.</label><graphic xlink:href="elife03430f007"/></fig></p><p>The results are essentially the same as in the original submission and we have now provided the reader with comprehensive access to the numerical results, including sequence alignments, list of all contact predictions, precision of predicted contacts with respect to known 3D structures for all complexes, docked models for 15 complexes,</p><p>Reviewer 1:</p><p><italic>1) The Abstract claims that the authors' approach can discriminate between interacting and non-interacting proteins. However, as far as I can see, the rest of the paper concerns only calculating the interface residues of proteins which are known to interact. No evidence is presented to support the claim to be able to calculate non-interactors. The authors' claim should be corrected accordingly</italic>.</p><p>We have updated the manuscript to clarify the way in which the method addresses discrimination between interacting and non-interacting proteins, and give the specific example of all against all in the ATP synthase complex. We suggest that the correct identification of interacting and non-interacting protein subunits of the ATP synthase complex could serve as a 'proof of principle' that scores derived from evolutionary couplings can identify interactions (in addition to the identification of the interacting residues between protein pairs). Since identification of the interactions of the 8 subunits of ATP synthase is the only example we report, we have been careful to talk about this as a proof of principle that may be generalized with further work (changes in Abstract, <xref ref-type="fig" rid="fig5">Figure 5</xref>, Materials and Methods, <xref ref-type="supplementary-material" rid="SD5-data">Supplementary file 5</xref>, Supplementary data). [The EV complex score identifies 24/28 of the interactions as correctly interacting or not.]</p><p><italic>2) The authors claim that the co-evolutionary approach has not previously been applied to prediction of protein-protein interfaces. This is incorrect, as the authors seem to be unaware of the previous work of Raphael Guerois' group, which seems rather surprising. The authors should acknowledge the prior work of Faure et al (2012) and Andreani et al. (2013), and they should modify their claim to novelty accordingly</italic>.</p><p><italic>It would also be appropriate to cite properly the prior work of the Baker group (Ovchinnikov et al., 2014) in the same paragraph (the authors currently mention this work only as a “note added during submission”), and the recent review by Andreani and Guerois (2014)</italic>.</p><p>We have now referred to the body of work by the Guerois group in the Introduction. We apologize for the oversight of this very interesting work. We also added more complete referencing to the work of the Valencia group; see response to reviewer 3. The Guerois group has used evolutionary information to improve their machine learnt statistical potentials. Our goal is to ask if we can we identify co-evolving residues (from sequence information alone) across proteins in order to ask whether these co-evolving pairs identify close residues, (1) whether they can be used to determine complexes in 3D and (2) whether we can use this to say if two proteins interact. Hence the approaches we present and those of the Guerois group are nicely synergistic and we hope to work with them to bring these methods together in the future.</p><p><italic>3) In several places the authors say that their approach exploits the fact that interacting proteins are often coded close to each other in a genome. Why is this assumption necessary? According to the description given in Methods, any pair of sequences which are presumed to interact could be concatenated and then used in the authors method. Please clarify</italic>.</p><p>Thanks for making it clear that we did not explain this sufficiently well. We have now clarified this in Results, Discussion, and in the Materials and methods.</p><p>To summarize: The accuracy of the co-evolutionary analysis relies on the concatenation of the protein pair representing a true interaction. This means that the contact prediction across proteins will only be as good as the input alignment pairs. When there is only one protein family member of both interacting partners in each species, one is guaranteed to get the correct alignment, assuming that it is a real complex in all organisms. Hence, subunits of ATP synthase that have only one copy in the genome, would not require this condition, and one could have simply concatenated the one pair per genome. However, for most protein interactions in <italic>E. coli</italic>, there are not yet enough sequences available to allow the use of just one pair per genome, as the complex may not necessarily occur in all bacteria. In these cases, for the time-being, our approach relies on using paralogous interactions to get sufficient sequences for instance histidine kinase; response regulators, transporters and their ATPases. Since we therefore use several paralogous interactions per complex in each genome, the algorithm requires that the partner needs to be correctly paired, something that we do not necessarily know <italic>a priori</italic>, and for which we use genome proximity as a proxy (as others have done in references 22-25). Clearly this problem will secede for many interactions in the next few years as many thousand more bacterial genomes are sequenced, but the problem is an interesting one that we think will have to be thought about in relation to eukaryotic complexes, too.</p><p><italic>4) If I understand the authors</italic>’ <italic>method correctly, they first concatenate the multiple sequences of the presumed interactors, and they then use their previous approach for detecting interacting pairs of columns in the multiple alignment. In this case, when concatenating the alignments for protein “A” with those of protein “B”, the “intra-EC” pairs would appear as A-A and B-B pairs, while the “inter-EC” pairs would come from A-B or B-A interactions. My question is then, are there any observable differences in the inter and intra scores? One might expect that the conservation scores would be lower for inter interactions than intra interactions, as an interface might show more “plasticity” than the core of a domain. It would be very interesting if the authors could comment on this, preferably supported by numerical results</italic>.</p><p>The reviewer makes a good point and one that we have now highlighted more clearly in the text. The inter-EC scores within each complex are almost universally lower than the intra–EC scores as would be expected, <xref ref-type="fig" rid="fig2">Figure 2</xref> and <xref ref-type="fig" rid="fig2s1">Figure 2–figure supplement 1</xref>.</p><p>In general we observe that the accuracy of the intra-contacts up to the rank of the first inter contact, is a good indication of how accurate the predicted inter-contacts are likely to be. This means we could have used a measure of the accuracy of the <italic>intra</italic>-protein scores to assess the predicted inter-contacts. We chose to develop a scoring method independent that did not rely on the existence of experimentally determined 3D structures of the monomers. The EV complex score implicitly considers where the inter-EC scores lie in the whole distribution instead, hence excluding those inter-ECs that lie within the noise of the whole distribution, see Materials and Methods (<xref ref-type="disp-formula" rid="equ1">equations 1</xref> and <xref ref-type="disp-formula" rid="equ2">2</xref>), <xref ref-type="fig" rid="fig2">Figure 2A</xref>, <xref ref-type="fig" rid="fig2s1">Figure 2–figure supplement 1</xref>, <xref ref-type="fig" rid="fig2s2">Figure 2–figure supplement 2</xref>, and Supplementary data 3 “EVcomplex predictions”.</p><p><italic>5) It is incorrect for the authors to refer to their own data set as a "benchmark". Suggestion: remove all references to the term "benchmark". However, if the authors make all their data available in a convenient way on-line, it could be proposed as a new "benchmark"</italic>.</p><p>We have removed the references to the set of known 3D interactions as ‘benchmark’ and proposed this as a set the community could use in the future, as the reviewer suggests (Materials and methods).</p><p><italic>6) It is wrong to claim that "Experimental evidence... agrees with EVcomplex predictions" (!). Please rewrite this to say that your predictions agree with the experimental evidence. But, if this is your claim, please also support it in some way. What is the experimental evidence? How to you calculate and quantify "agrees with"?</italic></p><p>We have removed this sentence, and reworded this to reflect the fact we are using the experimental data to support the EC predictions and not the other way around.</p><p><italic>7) Same point in the main text. "The resulting model is consistent with the topologies from cross-linking". How do you quantify consistent? RMSD from the earlier models? Please provide supporting details</italic>.</p><p>To our knowledge there are no experimentally determined atomic resolution structures of the a-subunit of ATP synthase. A 3D model of the a-subunit is from 1999 (PDB ID: 1c17) and was computed using five helical–helical interactions that were inferred from second suppressor mutation experiments, and then imposed as distance restraints for TMH2-5 [1], revealing a four helical bundle (with no information for TMH1). Later, zero-length cross-linking experiments by the Fillingame group [2] identified contacting residues from all pairs of helical combinations of TM2-TM5 (6), supporting the earlier 4 helical bundle topology. 7 of the 8 cross-linked pairs from Schwem et al., are either exactly the same pair (L120-I246) or adjacent to many pairs in the top L intra a-subunit evolutionary couplings (ECs)*, see <xref ref-type="fig" rid="fig7">Author response image 1</xref>. (Adjacent is defined as neighboring residues (±3) on chain or one helical turn.) * of ∼ L<sup>2</sup> total, see previous work and work of others for why this number is chosen.</p><p>Information from the cross-linking was not used to construct the model and no presumed membrane topology was used as input. The consistency we report is based on the correspondence between the helical-helical contacts from the experiments and evolutionary couplings together with the resulting contacts in the computed model. These can be examined in detail in the supplementary material. We have clarified this part of the analysis and provided more detail.</p><p>Reviewer 2:</p><p><italic>[…] I feel the paper could be substantially improved if the following points were addressed:</italic></p><p><italic>1) Please support the statement "Benchmark calculations here ... indicate that the number of sequences in the alignment is critical..." with a Figure showing overall performance versus # of sequences (</italic><xref ref-type="fig" rid="fig3"><italic>Figure 3</italic></xref> <italic>shows dependency of accuracy on relative rank for only two examples)</italic>.</p><p><italic>2) Show a main Figure comparing predicted contacts against residue distances in the 30 known crystal structures of complexes that had a sufficient number of sequences (</italic><xref ref-type="fig" rid="fig2"><italic>Figure 2</italic></xref> <italic>only shows contact plots for two examples, and structural pictures for several more, but no overall quantification). This type of analysis could also help to support the statement "For the top ranked benchmark complexes, the majority of the top 5 ECs is correct to within 8A..." with a more quantitative analysis (</italic><xref ref-type="table" rid="tbl1"><italic>Table 1</italic></xref> <italic>only shows 7 of the 30 complexes in the dataset;</italic> <xref ref-type="supplementary-material" rid="SD3-data"><italic>Supplementary file 3</italic></xref> <italic>shows all individual contact maps, but no overall quantification)</italic>.</p><p><italic>3) "... these benchmarks show ... and demonstrate the criteria needed for successful prediction of unknown interactions". To support this statement, it would be useful to have a main Figure / Table for each important criterion, analyzed over an entire benchmark set (as for the number of sequences in point 1)</italic>.</p><p>The claims in the paper are now supported by more explicit quantitative analysis, reported in the main figures, the text and supplementary material. Specifically we show a score that normalizes the ECs for the number of sequences and length of protein. This score allows a clear comparison of EC pairs across complexes so that one threshold can be applied across all complexes and precision can be measured for each complex and summarized overall. This material is provided in <xref ref-type="fig" rid="fig2">Figure 2</xref> and <xref ref-type="fig" rid="fig2s1 fig2s2">Figure 2–figure supplements 1 & 2</xref> (all EVcomplex scores, plots of raw scores showing length and number of sequences dependence, plots of EVcomplex scores versus accuracy), Supplementary data and Materials and methods.</p><p><italic>4) Please add metrics to support statements that ECs are "completely consistent" with crosslinking data, or that a coupling "coincides with experimental evidence". The comparison Table in Supplementary Figure 6 could be presented in more quantitative terms in the main text (for example, what does "crosslinking neighborhood" mean?)</italic>.</p><p>In summary, 77%/67% of the above threshold (13) predicted inter-protein contacts between subunit-a and subunit-b are in the neighborhood of residues identified in cross-linking studies, where neighborhood is defined as within 6/3 residues on the chain of the cross-linked residue (<xref ref-type="supplementary-material" rid="SD6-data">Supplementary file 6</xref>). The a239V- b16L cross-link is exactly one of the ECs. For 3/13 with no evidence, the proposed residue – residue contact between the subunits is consistent with the other cross-links: two are between midway on aTMH1 with midway of the membrane part of the b-subunit (aV50, aG53 with b13A), one is between aTMH3 and the N terminal end of the b-subunit (a155L, b7I) (these regions have not been tested to our knowledge). The 4<sup>th</sup> predicted EC with no cross-link support is between a66K and b68a. This EC is most likely a false positive as residue 68 in the b-subunit may be too far from the membrane surface to be plausible. Taking the body of work together from the experimental side [3-8], there are a number of specific regions of the a-subunit that are in contact with one or both of the b-monomers, and all of these regions are represented in the top evolutionary couplings; namely the first cytoplasmic loop, aTMH2, upper portion, aTMH3 and the periplasmic end of aTMH5, all of which are represented in the EVcomplex pairs (<xref ref-type="supplementary-material" rid="SD6-data">Supplementary file 6</xref>).</p><p>These clarifications are reflected in the main text and <xref ref-type="supplementary-material" rid="SD6-data">Supplementary file 6</xref>.</p><p>See reply to Reviewer 1 and <xref ref-type="fig" rid="fig7">Author response image 1</xref> for more detail on the ECs and crosslink studies within the a-subunit.</p><p><italic>5) What are the possible reasons for false-positive co-variation that does not correspond to contact?</italic></p><p>There are two categories of false positives:</p><p>1) There is co-evolution between residues that are not close in a 3D structure.</p><p>i) This could be functional coupling – e.g. cases of information transmission through membrane proteins, allosteric signaling and indeed we have seen this anecdotally in a number of very interesting cases. The challenge is to distinguish this from other false positives.</p><p>ii) The current crystal structures do not capture all the conformations of the protein(s). This is very clear in examples such as alternating-access membrane transporters that alter their conformations substantially</p><p>2) The assumptions used for the input sequence alignments are wrong</p><p>i) The interactions in the alignments are not homologous despite sequence similarity of the component parts.</p><p>ii) The sequence diversity is insufficient to capture realistic parameters in the global model.</p><p>Deconvolution of these different causes of false positives is a critical part of future work. We have made these points clearer in the Results and the Discussion.</p><p><italic>6) The manuscript deals entirely with pairwise co-evolution, and seems to neglect the possibility of higher-order complexity in the sequence pattern</italic>.</p><p>There could well be higher order correlations that the current method is unable to determine at this stage. The number of sequences needed for a global model such as this to determine accurate higher order covariation would be at least an order of magnitude higher than the requirement for the current method. Indeed there are insufficient sequences for many of the currently known <italic>E. coli</italic> interactions (Discussion) and see response to Reviewer 1 – comment 3. It will be interesting to see what the extent of this higher order dependence might be when enough sequences become available.</p><p>Reviewer 3:</p><p><italic>The manuscript presents an upbeat and optimistic view of the success of the method, with a relatively small amount of critical discussion and little if any investigation of what one can learn from cases in which it does not perform as expected</italic>.</p><p>We have updated the manuscript to include far more quantitative analysis, see replies to Reviewer 2 comments 1-4 above. We have also balanced the enthusiasm with a more specific description of the current limitations, that include sequence availability but also some that require algorithmic development (see Discussion). Critical discussion on the classification of false positives is now more clearly organized in the manuscript; see response to Reviewer 2, comment 5.</p><p><italic>(For example, a list of possible reasons for false-positive co-variation that does not correspond to contact is given, but an analysis of actual instances is not.) Likewise, a set of methods is presented that is relatively particular, and the reason why these specific methods were chosen over other possibilities is not provided</italic>.</p><p>There is a large body of work that has implemented other methods, both force field–based docking and other sequence based methods to explore co-variation e.g. mutual information and phylogeny to detect co-variation of residues across proteins. We have now added more discussion and references to this oeuvre in the Introduction, including new references to the body of work by the Valencia group that used correlations in multiple sequence alignments [9-10], and those suggested by Reviewer 1. Many other methods have addressed somewhat different issues, for instance, identification of interacting proteins (not residue level information), identification of residue patches rather than specific interactions, concentration on docking with hybrid approaches for known interactions or were relatively less successful (e.g. older work). For this reason it is hard to make direct comparisons. The unique aspect to this work is that it can resolve the question of interacting partners together with residue level information if the sequence diversity and space is sufficient. The EVcomplex approach, along with that of the recent work by the Baker group [11] also does this from sequences alone. Since experimentally determined structures may be a somewhat biased set of all protein interactions, our method has the advantage of not learning on known complex structures.</p><p>We look forward to the combination of the co-evolution approach together with existing computational and experimental approaches to accelerate the field.</p><p><italic>Moreover, the manuscript deals entirely with pairwise co-evolution, and seems to neglect the possibility of higher-order complexity in the sequence pattern. The manuscript could be substantially strengthened by adding analyses and insights in these issues</italic>.</p><p>See response to Reviewer 2, comment 6.</p><p><italic>References</italic></p><p>1 Rastogi, V. K. & Girvin, M. E. Structural changes linked to proton translocation by subunit c of the ATP synthase. <italic>Nature</italic> <bold>402</bold>, 263-268, <ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.1038/46224">doi:10.1038/46224</ext-link> (1999).</p><p>2 Schwem, B. 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