SMTL ID : 7lpe.1

Cryo-EM structure of full-length TRPV1 with capsaicin at 48 degrees Celsius, in an open state, class 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x LBN: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine(Non-covalent)

LBN.1: 7 residues within 4Å: Chain A: N.437, V.440, Y.441, Y.487, F.488, F.516, Y.555 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.440 Hydrogen bonds: A:N.437, A:Y.487, A:Y.555, A:Y.555 LBN.4: 7 residues within 4Å: Chain B: N.437, V.440, Y.441, Y.487, F.488, F.516, Y.555 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.440 Hydrogen bonds: B:N.437, B:Y.487, B:Y.555, B:Y.555 LBN.7: 7 residues within 4Å: Chain C: N.437, V.440, Y.441, Y.487, F.488, F.516, Y.555 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.440 Hydrogen bonds: C:N.437, C:Y.487, C:Y.555, C:Y.555 LBN.10: 7 residues within 4Å: Chain D: N.437, V.440, Y.441, Y.487, F.488, F.516, Y.555 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.440 Hydrogen bonds: D:N.437, D:Y.487, D:Y.555, D:Y.555

4 x 6OU: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate(Non-covalent)

6OU.2: 4 residues within 4Å: Chain A: Y.631, L.635, F.638 Chain D: L.664 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:Y.631, A:Y.631, A:L.635, A:F.638, D:L.664 6OU.5: 6 residues within 4Å: Chain A: A.657, I.661, L.664 Chain B: Y.631, L.635, F.638 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.661, A:L.664, B:Y.631, B:Y.631, B:L.635, B:F.638 6OU.8: 4 residues within 4Å: Chain B: L.664 Chain C: Y.631, L.635, F.638 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:L.664, C:Y.631, C:Y.631, C:L.635, C:F.638 6OU.11: 4 residues within 4Å: Chain C: L.664 Chain D: Y.631, L.635, F.638 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:L.664, D:Y.631, D:Y.631, D:L.635, D:F.638

4 x 4DY: (6E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide(Non-covalent)

4DY.3: 16 residues within 4Å: Chain A: Y.511, S.512, L.515, F.543, M.547, T.550, N.551, Y.554, R.557, A.566, E.570, I.573 Chain D: F.591, L.662, A.665, L.669 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:F.591, D:L.662, D:A.665, D:L.669, A:L.515, A:F.543 Hydrogen bonds: A:T.550, A:R.557 pi-Stacking: A:Y.511 4DY.6: 16 residues within 4Å: Chain A: F.591, L.662, A.665, L.669 Chain B: Y.511, S.512, L.515, F.543, M.547, T.550, N.551, Y.554, R.557, A.566, E.570, I.573 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.591, A:L.662, A:A.665, A:L.669, B:L.515, B:F.543 Hydrogen bonds: B:T.550, B:R.557 pi-Stacking: B:Y.511 4DY.9: 16 residues within 4Å: Chain B: F.591, L.662, A.665, L.669 Chain C: Y.511, S.512, L.515, F.543, M.547, T.550, N.551, Y.554, R.557, A.566, E.570, I.573 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:F.591, B:L.662, B:A.665, B:L.669, C:L.515, C:F.543 Hydrogen bonds: C:T.550, C:R.557 pi-Stacking: C:Y.511 4DY.12: 16 residues within 4Å: Chain C: F.591, L.662, A.665, L.669 Chain D: Y.511, S.512, L.515, F.543, M.547, T.550, N.551, Y.554, R.557, A.566, E.570, I.573 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:F.591, C:L.662, C:A.665, C:L.669, D:L.515, D:F.543 Hydrogen bonds: D:T.550, D:R.557 pi-Stacking: D:Y.511

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kwon, D.H. et al., Heat-dependent opening of TRPV1 in the presence of capsaicin. Nat.Struct.Mol.Biol. (2021)

Release Date

2021-07-28

Peptides

Transient receptor potential cation channel subfamily V member 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

C
A

D
D

Membrane

We predict this structure to be a membrane protein.
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Transient receptor potential cation channel subfamily V member 1

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