SMTL ID : 7lpd.1

Cryo-EM structure of full-length TRPV1 with capsaicin at 48 degrees Celsius, in an intermediate state, class 2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

LBN.1: 10 residues within 4Å: Chain A: N.437, V.440, G.484, Y.487, F.488, R.491, E.513, F.516, Y.554, Y.555 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.487, A:F.488 Hydrogen bonds: A:Y.555 Salt bridges: A:R.491, A:E.513 LBN.6: 3 residues within 4Å: Chain A: Y.454, F.473, G.477 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.473 LBN.8: 10 residues within 4Å: Chain B: N.437, V.440, G.484, Y.487, F.488, R.491, E.513, F.516, Y.554, Y.555 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.487, B:F.488 Hydrogen bonds: B:Y.555 Salt bridges: B:R.491, B:E.513 LBN.13: 3 residues within 4Å: Chain B: Y.454, F.473, G.477 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.473 LBN.14: 10 residues within 4Å: Chain C: N.437, V.440, G.484, Y.487, F.488, R.491, E.513, F.516, Y.554, Y.555 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.487, C:F.488 Hydrogen bonds: C:Y.555 Salt bridges: C:R.491, C:E.513 LBN.19: 3 residues within 4Å: Chain C: Y.454, F.473, G.477 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.473 LBN.20: 10 residues within 4Å: Chain D: N.437, V.440, G.484, Y.487, F.488, R.491, E.513, F.516, Y.554, Y.555 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:Y.487, D:F.488 Hydrogen bonds: D:Y.555 Salt bridges: D:R.491, D:E.513 LBN.24: 3 residues within 4Å: Chain D: Y.454, F.473, G.477 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.473

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

6OU.2: 8 residues within 4Å: Chain A: L.585, Y.631 Chain D: K.656, A.657, I.660, L.664 Ligands: 6OU.3, 6OU.23 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:A.657, D:I.660, D:L.664, A:L.585 6OU.3: 6 residues within 4Å: Chain A: F.589, S.629, L.630 Chain B: Y.453, Y.454 Ligands: 6OU.2 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.589 Hydrogen bonds: A:S.629, A:L.630, B:Y.454 6OU.5: 7 residues within 4Å: Chain A: F.655, K.656, A.657, V.658, I.661 Chain B: F.522 Ligands: 6OU.9 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.522, A:A.657, A:I.661 Hydrogen bonds: A:K.656, A:A.657 6OU.7: 6 residues within 4Å: Chain A: Y.453, Y.454 Chain D: F.589, S.629, L.630 Ligands: 6OU.21 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:F.589 Hydrogen bonds: D:S.629, D:L.630, A:Y.454 6OU.9: 7 residues within 4Å: Chain A: K.656, I.660, L.664 Chain B: L.585, Y.631 Ligands: 6OU.5, 6OU.10 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.660, A:L.664, B:L.585 6OU.10: 6 residues within 4Å: Chain B: F.589, S.629, L.630 Chain C: Y.453, Y.454 Ligands: 6OU.9 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.589 Hydrogen bonds: B:S.629, B:L.630, C:Y.454 6OU.12: 7 residues within 4Å: Chain B: F.655, K.656, A.657, V.658, I.661 Chain C: F.522 Ligands: 6OU.15 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:A.657, B:I.661, C:F.522 Hydrogen bonds: B:K.656, B:A.657 6OU.15: 7 residues within 4Å: Chain B: K.656, I.660, L.664 Chain C: L.585, Y.631 Ligands: 6OU.12, 6OU.16 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.660, B:L.664, C:L.585 6OU.16: 6 residues within 4Å: Chain C: F.589, S.629, L.630 Chain D: Y.453, Y.454 Ligands: 6OU.15 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.589 Hydrogen bonds: C:S.629, C:L.630, D:Y.454 6OU.18: 7 residues within 4Å: Chain C: F.655, K.656, A.657, V.658, I.661 Chain D: F.522 Ligands: 6OU.21 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:A.657, C:I.661, D:F.522 Hydrogen bonds: C:K.656, C:A.657 6OU.21: 8 residues within 4Å: Chain C: K.656, A.657, I.660, L.664 Chain D: L.585, Y.631 Ligands: 6OU.7, 6OU.18 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.585, C:A.657, C:I.660, C:L.664 6OU.23: 7 residues within 4Å: Chain A: F.522 Chain D: F.655, K.656, A.657, V.658, I.661 Ligands: 6OU.2 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:A.657, D:I.661, A:F.522 Hydrogen bonds: D:K.656, D:A.657

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

4DY.4: 14 residues within 4Å: Chain A: Y.511, S.512, L.515, F.543, A.546, T.550, N.551, L.553, Y.554, R.557, I.573 Chain D: F.591, L.662, L.669 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:A.546, A:L.553, D:F.591, D:F.591, D:L.662, D:L.669 Hydrogen bonds: A:Y.511, A:T.550, A:R.557, A:E.570 4DY.11: 14 residues within 4Å: Chain A: F.591, L.662, L.669 Chain B: Y.511, S.512, L.515, F.543, A.546, T.550, N.551, L.553, Y.554, R.557, I.573 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:F.591, A:F.591, A:L.662, A:L.669, B:A.546, B:L.553 Hydrogen bonds: B:Y.511, B:T.550, B:R.557, B:E.570 4DY.17: 14 residues within 4Å: Chain B: F.591, L.662, L.669 Chain C: Y.511, S.512, L.515, F.543, A.546, T.550, N.551, L.553, Y.554, R.557, I.573 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:A.546, C:L.553, B:F.591, B:F.591, B:L.662, B:L.669 Hydrogen bonds: C:Y.511, C:T.550, C:R.557, C:E.570 4DY.22: 14 residues within 4Å: Chain C: F.591, L.662, L.669 Chain D: Y.511, S.512, L.515, F.543, A.546, T.550, N.551, L.553, Y.554, R.557, I.573 10 PLIP interactions: 6 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:A.546, D:L.553, C:F.591, C:F.591, C:L.662, C:L.669 Hydrogen bonds: D:Y.511, D:T.550, D:R.557, D:E.570

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
A

B
B

C
C

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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