SMTL ID : 7lpc.1

Cryo-EM structure of full-length TRPV1 at 48 degrees Celsius

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.06 Å

Oligo State

homo-tetramer

Ligands

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

6OU.1: 7 residues within 4Å: Chain A: I.446, Y.453, Y.454, W.549 Chain C: F.589, L.630 Ligands: 6OU.26 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:I.446, A:Y.454, A:W.549, C:F.589, C:F.589, C:F.589, C:F.589 Hydrogen bonds: A:Y.453, A:Y.454 6OU.6: 6 residues within 4Å: Chain A: S.629, Y.631, F.638 Chain C: A.657 Ligands: 6OU.30, 6OU.31 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.631, A:Y.631, A:Y.631, A:F.638, A:F.638 Hydrogen bonds: A:S.629 6OU.7: 5 residues within 4Å: Chain A: Y.511, L.574, R.575, C.578 Ligands: 6OU.8 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.571, A:R.575 6OU.8: 5 residues within 4Å: Chain A: C.578, R.579, L.585 Ligands: 6OU.7, YFP.33 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.579, A:L.585 6OU.9: 6 residues within 4Å: Chain A: F.448, E.478, V.482, M.523, Y.530, M.541 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.448, A:E.478, A:V.482, A:Y.530, A:Y.530 6OU.10: 7 residues within 4Å: Chain A: D.654, F.655, K.656, A.657, I.661 Ligands: T7X.34, 6OU.36 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.661 Hydrogen bonds: A:D.654, A:K.656, A:A.657 6OU.11: 7 residues within 4Å: Chain B: I.446, Y.453, Y.454, W.549 Chain D: F.589, L.630 Ligands: 6OU.36 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:I.446, B:Y.454, B:W.549, D:F.589, D:F.589, D:F.589, D:F.589 Hydrogen bonds: B:Y.453, B:Y.454 6OU.16: 7 residues within 4Å: Chain B: S.629, Y.631, F.638 Chain D: A.657, L.664 Ligands: 6OU.21, 6OU.40 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:L.664, B:Y.631, B:Y.631, B:Y.631, B:F.638, B:F.638 Hydrogen bonds: B:S.629 6OU.17: 5 residues within 4Å: Chain B: Y.511, L.574, R.575, C.578 Ligands: 6OU.18 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.571, B:R.575 6OU.18: 7 residues within 4Å: Chain B: C.578, R.579, L.585 Chain C: Q.561, M.562 Ligands: 6OU.17, YFP.23 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:Q.561, B:R.579, B:L.585 6OU.19: 6 residues within 4Å: Chain B: F.448, E.478, V.482, M.523, Y.530, M.541 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.448, B:E.478, B:V.482, B:Y.530, B:Y.530 6OU.20: 6 residues within 4Å: Chain B: D.654, F.655, K.656, A.657, I.661 Ligands: 6OU.26 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.661 Hydrogen bonds: B:D.654, B:K.656, B:A.657 6OU.21: 7 residues within 4Å: Chain B: F.589, L.630 Chain C: I.446, Y.453, Y.454, W.549 Ligands: 6OU.16 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:I.446, C:Y.454, C:W.549, B:F.589, B:F.589, B:F.589, B:F.589 Hydrogen bonds: C:Y.453, C:Y.454 6OU.26: 8 residues within 4Å: Chain B: A.657, I.661, L.664 Chain C: S.629, Y.631, F.638 Ligands: 6OU.1, 6OU.20 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:A.657, B:I.661, B:L.664, C:Y.631, C:Y.631, C:Y.631, C:F.638, C:F.638 Hydrogen bonds: C:S.629 6OU.27: 5 residues within 4Å: Chain C: Y.511, L.574, R.575, C.578 Ligands: 6OU.28 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:K.571, C:R.575 6OU.28: 7 residues within 4Å: Chain A: Q.561, M.562 Chain C: C.578, R.579, L.585 Ligands: YFP.3, 6OU.27 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:Q.561, C:R.579, C:L.585 6OU.29: 6 residues within 4Å: Chain C: F.448, E.478, V.482, M.523, Y.530, M.541 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.448, C:E.478, C:V.482, C:Y.530, C:Y.530 6OU.30: 6 residues within 4Å: Chain C: D.654, F.655, K.656, A.657, I.661 Ligands: 6OU.6 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.661 Hydrogen bonds: C:D.654, C:K.656, C:A.657 6OU.31: 7 residues within 4Å: Chain A: F.589, L.630 Chain D: I.446, Y.453, Y.454, W.549 Ligands: 6OU.6 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:I.446, D:Y.454, D:W.549, A:F.589, A:F.589, A:F.589, A:F.589 Hydrogen bonds: D:Y.453, D:Y.454 6OU.36: 6 residues within 4Å: Chain A: L.664 Chain D: S.629, Y.631, F.638 Ligands: 6OU.10, 6OU.11 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: A:L.664, A:L.664, D:Y.631, D:Y.631, D:Y.631, D:F.638, D:F.638 Hydrogen bonds: D:S.629 6OU.37: 5 residues within 4Å: Chain D: Y.511, L.574, R.575, C.578 Ligands: 6OU.38 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:K.571, D:R.575 6OU.38: 6 residues within 4Å: Chain B: Q.561 Chain D: C.578, R.579, L.585 Ligands: YFP.13, 6OU.37 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:Q.561, D:R.579, D:L.585 6OU.39: 6 residues within 4Å: Chain D: F.448, E.478, V.482, M.523, Y.530, M.541 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.448, D:E.478, D:V.482, D:Y.530, D:Y.530 6OU.40: 6 residues within 4Å: Chain D: D.654, F.655, K.656, A.657, I.661 Ligands: 6OU.16 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.661 Hydrogen bonds: D:D.654, D:K.656, D:A.657

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

LBN.2: 7 residues within 4Å: Chain A: L.443, I.446, I.447, Y.454, G.470, F.473, T.476 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.443, A:I.446, A:I.447, A:Y.454, A:Y.454, A:T.476 LBN.5: 13 residues within 4Å: Chain A: N.437, V.440, Y.441, S.483, G.484, Y.487, F.488, R.491, S.512, E.513, F.516, Y.554, Y.555 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.440, A:Y.487 Hydrogen bonds: A:Y.487, A:Y.555 Salt bridges: A:R.491, A:E.513 pi-Cation interactions: A:F.516, A:Y.554 LBN.12: 7 residues within 4Å: Chain B: L.443, I.446, I.447, Y.454, G.470, F.473, T.476 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.443, B:I.446, B:I.447, B:Y.454, B:Y.454, B:T.476 LBN.15: 13 residues within 4Å: Chain B: N.437, V.440, Y.441, S.483, G.484, Y.487, F.488, R.491, S.512, E.513, F.516, Y.554, Y.555 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.440, B:Y.487 Hydrogen bonds: B:Y.487, B:Y.555 Salt bridges: B:R.491, B:E.513 pi-Cation interactions: B:F.516, B:Y.554 LBN.22: 7 residues within 4Å: Chain C: L.443, I.446, I.447, Y.454, G.470, F.473, T.476 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.443, C:I.446, C:I.447, C:Y.454, C:Y.454, C:T.476 LBN.25: 13 residues within 4Å: Chain C: N.437, V.440, Y.441, S.483, G.484, Y.487, F.488, R.491, S.512, E.513, F.516, Y.554, Y.555 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:V.440, C:Y.487 Hydrogen bonds: C:Y.487, C:Y.555 Salt bridges: C:R.491, C:E.513 pi-Cation interactions: C:F.516, C:Y.554 LBN.32: 7 residues within 4Å: Chain D: L.443, I.446, I.447, Y.454, G.470, F.473, T.476 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.443, D:I.446, D:I.447, D:Y.454, D:Y.454, D:T.476 LBN.35: 13 residues within 4Å: Chain D: N.437, V.440, Y.441, S.483, G.484, Y.487, F.488, R.491, S.512, E.513, F.516, Y.554, Y.555 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:V.440, D:Y.487 Hydrogen bonds: D:Y.487, D:Y.555 Salt bridges: D:R.491, D:E.513 pi-Cation interactions: D:F.516, D:Y.554

4 x YFP: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol(Non-covalent)

YFP.3: 11 residues within 4Å: Chain A: Y.435, F.438, F.439, C.442, L.443, G.558, F.559, Q.560, M.562 Chain C: F.582 Ligands: 6OU.28 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:Y.435, A:Y.435, A:F.438, A:F.439, A:F.439, A:L.443, A:F.559, C:F.582 Hydrogen bonds: A:Y.435, A:Q.560 YFP.13: 11 residues within 4Å: Chain B: Y.435, F.438, F.439, C.442, L.443, G.558, F.559, Q.560, M.562 Chain D: F.582 Ligands: 6OU.38 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:Y.435, B:Y.435, B:F.438, B:F.439, B:F.439, B:L.443, B:F.559, D:F.582 Hydrogen bonds: B:Y.435, B:Q.560 YFP.23: 10 residues within 4Å: Chain C: Y.435, F.438, F.439, C.442, L.443, G.558, F.559, Q.560, M.562 Ligands: 6OU.18 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:Y.435, C:Y.435, C:F.438, C:F.439, C:F.439, C:L.443, C:F.559 Hydrogen bonds: C:Y.435, C:Q.560 YFP.33: 11 residues within 4Å: Chain A: F.582 Chain D: Y.435, F.438, F.439, C.442, L.443, G.558, F.559, Q.560, M.562 Ligands: 6OU.8 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:Y.435, D:Y.435, D:F.438, D:F.439, D:F.439, D:L.443, D:F.559, A:F.582, A:F.582 Hydrogen bonds: D:Y.435, D:Q.560

4 x T7X: Phosphatidylinositol(Non-covalent)

T7X.4: 14 residues within 4Å: Chain A: R.409, D.509, S.510, Y.511, S.512, L.515, M.547, T.550, N.551, L.553, R.557, E.570, I.696, Q.700 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.511, A:L.515, A:L.553, A:E.570 Hydrogen bonds: A:R.409, A:R.409, A:Y.511, A:S.512, A:K.571, A:Q.700 Salt bridges: A:R.557 T7X.14: 14 residues within 4Å: Chain B: R.409, D.509, S.510, Y.511, S.512, L.515, M.547, T.550, N.551, L.553, R.557, E.570, I.696, Q.700 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.511, B:L.515, B:L.553, B:E.570 Hydrogen bonds: B:R.409, B:R.409, B:Y.511, B:S.512, B:K.571, B:Q.700 Salt bridges: B:R.557 T7X.24: 14 residues within 4Å: Chain C: R.409, D.509, S.510, Y.511, S.512, L.515, M.547, T.550, N.551, L.553, R.557, E.570, I.696, Q.700 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:Y.511, C:L.515, C:L.553, C:E.570 Hydrogen bonds: C:R.409, C:R.409, C:Y.511, C:S.512, C:K.571, C:Q.700 Salt bridges: C:R.557 T7X.34: 15 residues within 4Å: Chain D: R.409, D.509, S.510, Y.511, S.512, L.515, M.547, T.550, N.551, L.553, R.557, E.570, I.696, Q.700 Ligands: 6OU.10 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:Y.511, D:L.515, D:L.553, D:E.570 Hydrogen bonds: D:R.409, D:R.409, D:Y.511, D:S.512, D:K.571, D:Q.700 Salt bridges: D:R.557

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
A

C
B

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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