This project is a part of my rna-tools, so please cite this paper if you find this repository useful for you:
Magnus M, Antczak M, Zok T, Wiedemann J, Lukasiak P, Cao Y, Bujnicki JM,
Westhof E, Szachniuk M, Miao Z.
RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets,
structure manipulation, and evaluation tools.
Nucleic Acids Research. 2019 10.1093/nar/gkz1108
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz1108/5651330
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- Acknowledgement
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Created by gh-md-toc
Processed PyMOL session of cryo-em structures, see https://github.com/mmagnus/PyMOL4Spliceosome/releases to learn more about current stage of the project.
The session now is very big and it might slow your computer. We recommend to open it one, remove unnecessary things for your analysis and save it as a new session.
(BTW, the intron here is in black, it's fixed in the version 0.31, now the intron is in gray)
The structures superimposed based on the U6 RNA (if possible) or Prp8.
Colors and chain mapping based on Spliceosome_PyMOL prepared by Eysmont and Magnus, merged with https://github.com/maxewilkinson/Spliceosome-PyMOL-sessions.
Not everything is perfect, expect some updates soon.
See https://github.com/mmagnus/PyMOL4Spliceosome/releases
and read more about the tool used to obtain this session: https://github.com/mmagnus/rna-tools/blob/master/rna_tools/tools/PyMOL4RNA/
All processed structures can be viewed and searched in this repository:
https://github.com/mmagnus/rna-tools/blob/master/rna_tools/tools/PyMOL4RNA/Spliceosome_PyMOL.csv
| Processed? | Complex | PDB ID | Resolution (Å) | Lab | Reference |
|---|---|---|---|---|---|
| x | E | 6N7P | 3.6 | Rui Zhao | Li et al. (2019) |
| x | E | 6N7R | 3.20 | Rui Zhao | Li et al. (2019) |
| x | Tri-snRNP | 5GAN | 3.7 | Kiyoshi Nagai | Nguyen et al. (2016) |
| #todo | Pre-B | 5ZWM | 3.4 | Yigong Shi | Bai et al. (2018) |
| x | B | 5ZWO | 3.9 | Yigong Shi | Bai et al. (2018) |
| x | Bact | 5GM6 | 3.5 | Yigong Shi | Yan et al. (2016) |
| x | C | 5LJ3 | 3.8 | Kiyoshi Nagai | Galej et al. (2016) |
| x | C | 5GMK | 3.85 | Yigong Shi | Wan et al. (2016) |
| x | C* | 5MPS | 3.85 | Kiyoshi Nagai | Fica et al. (2017) |
| x | P | 5YLZ | 3.6 | Yigong Shi | Bai et al. (2017) |
| x | P | 6EXN | 3.7 | Kiyoshi Nagai | Wilkinson et al. (2017) |
| x | ILS | 5Y88 | 3.5 | Yigong Shi | Wan et al. (2017) |
| - | ILS | 3JB9 | 3.60 | Yigong Shi | Yan et al. (2015) |
Adapted and updated: L. Zhang, A. Vielle, S. Espinosa, and R. Zhao, “RNAs in the spliceosome: Insight from cryoEM structures,” WIREs RNA, vol. 10, no. 3, pp. e1523–11, Apr. 2019.
A unified mechanism for intron and exon definition and back-splicing.
Li, X., Liu, S., Zhang, L., Issaian, A., Hill, R.C., Espinosa, S., Shi, S., Cui, Y., Kappel, K., Das, R., Hansen, K.C., Zhou, Z.H., Zhao, R.
(2019) Nature 573: 375-380
6N7P: S. cerevisiae spliceosomal E complex (UBC4)
6N7R: S. cerevisiae spliceosomal E complex (ACT1)
Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 angstrom resolution.
Nguyen, T.H., Galej, W.P., Bai, X.C., Oubridge, C., Newman, A.J., Scheres, S.H., Nagai, K.
(2016) Nature 530: 298-302
5GAN: The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP at 3.7 Angstrom
Structures of the fully assembled Saccharomyces cerevisiae spliceosome before activation
Bai, R., Wan, R., Yan, C., Lei, J., Shi, Y.
(2018) Science 360: 1423-1429
5ZWM: Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.4~4.6 angstrom (tri-snRNP and U2 snRNP Part)
5ZWO: Cryo-EM structure of the yeast B complex at average resolution of 3.9 angstrom
Structure of a yeast activated spliceosome at 3.5 angstrom resolution
Yan, C., Wan, R., Bai, R., Huang, G., Shi, Y.
(2016) Science 353: 904-911
5GM6 Cryo-EM structure of the activated spliceosome (Bact complex) at 3.5 angstrom resolution
Cryo-EM structure of the spliceosome immediately after branching.
Galej, W.P., Wilkinson, M.E., Fica, S.M., Oubridge, C., Newman, A.J., Nagai, K.
(2016) Nature 537: 197-201
5LJ3:Structure of the core of the yeast spliceosome immediately after branching
Structure of a yeast catalytic step I spliceosome at 3.4 angstrom resolution Wan, R., Yan, C., Bai, R., Huang, G., Shi, Y. (2016) Science 353: 895-904 5GMK: Cryo-EM structure of the Catalytic Step I spliceosome (C complex) at 3.4 angstrom resolution
Structure of a spliceosome remodelled for exon ligation.
Fica, S.M., Oubridge, C., Galej, W.P., Wilkinson, M.E., Bai, X.C., Newman, A.J., Nagai, K.
(2017) Nature 542: 377-380
5MPS: Structure of a spliceosome remodeled for exon ligation
Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae
Bai, R., Yan, C., Wan, R., Lei, J., Shi, Y.
(2017) Cell 171: 1589-1598.e8
5YLZ: Cr yo-EM Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae at 3.6 angstrom
Postcatalytic spliceosome structure reveals mechanism of 3'-splice site selection.
Wilkinson, M.E., Fica, S.M., Galej, W.P., Norman, C.M., Newman, A.J., Nagai, K.
(2017) Science 358: 1283-1288
6EXN: Post-catalytic P complex spliceosome with 3' splice site docked
Structure of an Intron Lariat Spliceosome from Saccharomyces cerevisiae
Wan, R., Yan, C., Bai, R., Lei, J., Shi, Y.
(2017) Cell 171: 120-132
5Y88: Cryo-EM structure of the intron-lariat spliceosome ready for disassembly from S.cerevisiae at 3.5 angstrom
Structure of a yeast spliceosome at 3.6-angstrom resolution Yan, C., Hang, J., Wan, R., Huang, M., Wong, C., Shi, Y. (2015) Science 349: 1182-1191 3JB9: Cryo-EM structure of the yeast spliceosome at 3.6 angstrom resolution
| x | Complex | PDB ID | Resolution (Å) | Lab | Reference |
|---|---|---|---|---|---|
| x | Tri-snRNP | 6QW6 | 2.92 | Kiyoshi Nagai | Charenton et al. (2019) |
| x | Pre-B | 6QX9 | 3.28 | Kiyoshi Nagai | Charenton et al. (2019) |
| x | B | 6AHD | 3.80 | Yigong Shi | Zhan et al. (2018) |
5XJC Cryo-EM structure of the human spliceosome just prior to exon ligation at 3.6 angstrom
An Atomic Structure of the Human Spliceosome Zhang, X., Yan, C., Hang, J., Finci, L.I., Lei, J., Shi, Y. (2017) Cell 169: 918-929.e14 5XJC Cryo-EM structure of the human spliceosome just prior to exon ligation at 3.6 angstrom
*Mechanism of 5' splice site transfer for human spliceosome activation. *
Charenton, C., Wilkinson, M.E., Nagai, K.
(2019) Science 364: 362-367
6QW6: Structure of the human U5.U4/U6 tri-snRNP at 2.9A resolution.
6QX9: Structure of a human fully-assembled precatalytic spliceosome (pre-B complex).
*Structures of the human pre-catalytic spliceosome and its precursor spliceosome. *
Zhan, X., Yan, C., Zhang, X., Lei, J., Shi, Y.
(2018) Cell Res 28: 1129-1140
6AHD: The Cryo-EM Structure of Human Pre-catalytic Spliceosome (B complex) at 3.8 angstrom resolution
| x | Complex | PDB ID | Resolution (Å) | Lab | Reference |
|---|---|---|---|---|---|
| x | ILS | 3JB9 | 3.60 | Yigong Shi | Yuan et al. (2015) |
Structure of a yeast spliceosome at 3.6-angstrom resolution__ Yan, C., Hang, J., Wan, R., Huang, M., Wong, C., Shi, Y. (2015) Science 349: 1182-1191
Assembly, catalytic activation, and disassembly pathway of the spliceosome. For simplicity, the ordered interactions of the U1, U2, U4/
U6, and U5 small nuclear ribonucleoproteins (snRNPs), but not non-snRNP spliceosomal proteins, are shown.
Helicases required for splicing in both yeast and humans are indicated and include the Ski2-like helicase BBR2, the
DEAD-box helicases UAP56, PRP5, and PRP28, and the DEAH-box helicases PRP2, PRP16, PRP22, and PRP43. (D)
Dynamic network of RNA–RNA interactions in the spliceosomal B and Bact complexes. (E) 3D structure of the
catalytic RNA network (in the human C∗ complex), showing the coordination of the catalytic magnesium ions M1
and M2. (F) Dynamic exchange of spliceosomal proteins during splicing. Proteins present in pre-B, B, Bact, C, or C∗
human spliceosomal complexes are indicated by a square, in which blue denotes highly abundant and gray moder-
ately abundant proteins. Serine-arginine (SR) dipeptide-rich proteins and heterogeneous nuclear ribonucleoproteins
(hnRNPs), as well as those present in very low amounts, are not shown. The table summarizes the proteomes of
various, recently purified human spliceosomal complexes (Agafonov et al. 2011; De et al. 2015; Boesler et al. 2016; Bertram et al. 2017b), as well as our unpublished work.
*Prp38 and Snu23 are associated with the tri-snRNP in S. cerevisiae. (G) Differential pre-organization of yeast nineteen complex (NTC) proteins in humans.
Source: B. Kastner, C. L. Will, H. Stark, and R. Luhrmann, “Structural Insights into Nuclear pre-mRNA Splicing in Higher Eukaryotes.,” Cold Spring Harbor Perspectives in Biology, pp. a032417–20, Feb. 2019.
With Up Down with Righ-mouse Click
PyMOL>enable CWC15*
PyMOL>disable CWC15*
# select only some objects and save it to the file
save /Users/magnus/Desktop/XXXX_triplex_zoom.pse, CXXX_P and U2_P and U6_P
select U4* and resi 68-81
Read more: https://pymolwiki.org/index.php/Enable
You can also download sessions for single steps prepared by the Nagai lab: https://www2.mrc-lmb.cam.ac.uk/groups/nagai/resources/ and here https://github.com/maxewilkinson/Spliceosome-PyMOL-sessions
200820 Format for objects: <protein(uppercase)><organism: [y h]><stage [yC yCs]><pdb_id(uppercase)>, .e.g, CWC15_yC_5GMK
save aligned/hB_6AHD.pdb, PRP_hB_6AHD
align h3_6QW6 and chain 5A, PRP8_hB_6AHD
save
fetch 6QX9
align 6QX9 and chain 5A, PRP8_hB_6AHD
save hBpre_6QX9.cif, 6QX9
fetch 6QW6
align 6QW6 and chain 5A, PRP8_hB_6AHD
save h3_6QW6.cif, 6QW6
PyMOL> align yC_5GMK and chain A, PRP8*
PyMOL>save yC_5GMK.cif, yC_5GMK
Save: wrote "yC_5GMK.cif".
align hC_5YZG and chain F, U6_yC_5GMK
save hC_5YZG.cif, hC_5YZG
align 5XJC and chain F, U6_*
save hCs_5XJC.cif, 5XJC
Rings as one object
extract Lsm_ring_h3_6QW6, (chain 62 and h3_6QW6) or (chain 64 and h3_6QW6)
extract Lsm_ring_h3_6QW6, (chain 62 or chain 64) and h3_6QW6
Sandbox
PyMOL>select chain 5A and name hBpre_6QX9
Selector: selection "sele" defined with 0 atoms.
PyMOL>extract SM_ring, SM*
Save: Please wait -- writing session file...
Save: wrote "/Users/magnus/work/src/rna-tools/rna_tools/tools/PyMOL4RNA/PyMOL4Spliceosome/release/yCs_5MPS.pse".
- remove exons
ReMedy-International Research Agenda Unit, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
M.M. was supported by the "Regenerative Mechanisms for Health-ReMedy" grant MAB/20172, carried out within the International Research Agendas Program of the Foundation for Polish Science co-financed by the European Union under the European Regional Development Fund.
Full list: http://spliceosomedb.ucsc.edu/structures
Source: L. Zhang, A. Vielle, S. Espinosa, and R. Zhao, “RNAs in the spliceosome: Insight from cryoEM structures,” WIREs RNA, vol. 10, no. 3, pp. e1523–11, Apr. 2019.
Source: L. Zhang, A. Vielle, S. Espinosa, and R. Zhao, “RNAs in the spliceosome: Insight from cryoEM structures,” WIREs RNA, vol. 10, no. 3, pp. e1523–11, Apr. 2019.