Cryo-EM structure of the full-length TRPV1 with rtx at 4 degrees celsius, in a closed state, class I

Structure

electron microscopy · 1 distinct chain · 58% helix, 4% strand (DSSP).

Ligands and binding sites

• 6OU · [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate · ligand · 20 copies · chains A, B, D, C
• LBN · 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine · ligand · 8 copies · chains A, D, C, B
• 6EU · resiniferatoxin · ligand · 4 copies · chains A, D, C, B
• YFP · 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol · ligand · 4 copies · chains A, D, C, B
• NA · Sodium ion · metal · 2 copies · chains A, C, B, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• C–B · 2695 Ų buried · 7 hydrogen bonds · protein-protein
• A–D · 2695 Ų buried · 7 hydrogen bonds · protein-protein
• A–B · 2693 Ų buried · 7 hydrogen bonds · protein-protein
• C–D · 2690 Ų buried · 7 hydrogen bonds · protein-protein
• B–D · 12 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

• 7RQU · Cryo-EM structure of the full-length TRPV1 with RTx at 4 degrees Celsius, in a closed… · the same entry in another collection · chain A against A, TM-score 1.00
• O35433 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.95

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt O35433
• Elsewhere: RCSB PDB 7RQU · PDBe 7RQU · UniProt O35433