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Structures

Structure browser

The structure table shows an annotated list of published GPCR structures. The table can be sorted by each column by clicking on the header. The search fields below each header can be used to filter the structures, e.g. show only those with a co-crystallized agonist or X-ray resolution < 2.5 Å.

To view an alignment of the structures' sequences, click the "View alignment" button.

Structure state

A Δ distance was determined for all class A structure templates by subtracting the 3x44-7x52 C alpha distance from the 2x41-6x38 C alpha distance and for all class B structure templates by subtracting the 3x44-7x51 C alpha distance from the 2x41-6x33 C alpha distance. These values are now provided in the Structure Browser (gpcrdb.org/structure) in the Δ distance (Å) column.

TM2 TM6 TM3 TM7 Class Inactive Intermediate Active
2x41 6x38 3x44 7x52 A <2 2<=x<=7.15 >7.15
2x41 6x33 3x44 7x51 B <2.5 2.5<=x<=6 >6

All Class C and F structures are, so far, in the inactive state.

This definition is an approach more based on structure than function. The Δ distance resembles a general openness of the intracellular side of the receptor where coupling of a signaling protein can occur. There are structures where based on ligand properties the structure should be identified as inactive, however due to a fusion protein on the intracellular side of the receptor, the conformation is more similar to an active structure (e.g. 5NDD, 5NJ6). Another unusual example is one of the Platelet-activating factor receptor structures (5ZKP), where H8 turns inward the helical bundle, blocking the chance of signal protein coupling while pushing TM2 outwards.

Structure statistics

The statistics page shown a bar graph showing the number of structures available by year (and grouped by the endogenous ligand type of the receptors), a bar graph showing the resolution ranges of the available structures, and phylogenetic trees for each receptor class, with receptors with determined structures highlighted.

The graphs are automatically updated when new data is added to GPCRdb, making them ideal for use in publications and presentations.

Structure superposition

The superposition tool allows users to upload two or more structures (or models) and superpose them based on a user-specified segment selection. Using the tool is a two step process.

  1. Select structures to upload. Only on reference structure can be uploaded, but multiple structures to superpose on the reference can be uploaded. To select many structures for upload, hold down the Control key (or Command on Mac) while selecting
  2. After structures have been uploaded, the user is presented with a sequence segment selection page. The user can select one or more sequence segments, and/or expand each segment to select the residues within it individually. Residues selected individually are grouped into a custom sequence segment.

PDB file residue numbering

The PDB file residue numbering tool adds generic residue numbers from GPCRdb to any GPCR structure or model. This can be useful when comparing structures visually.

A user simply uploads her structure and downloads a modified version of that structure, where b factors of certain atoms have been replaced with generic numbers. Note that CA atoms will be assigned a number in GPCRdb notation, and N atoms will be annotated with Ballesteros-Weinstein scheme.

On the structure download page, users can download scripts to visualize the generic numbers in PyMOL and Maestro.

Template selection

Using the template selection tool is a one step process. The user is first presented with a reference receptor selection page. The selected reference receptor will be compared to the published GPCR structures, making it a useful tool for selecting templates for homology modeling.

Once a reference receptor has been selected, an annotated table of published GPCR structures, ranked by similarity to the selected reference receptor is shown. The table can be sorted by each column by clicking on the header. The search fields below each header can be used to filter the structures, e.g. show only those with a co-crystallized agonist or X-ray resolution < 2.5 Å.