SMTL ID : 9p6b.1

Cryo-EM structure of full-length human TRPV1 in the presence of alpha-humulene

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

32 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.1: 19 residues within 4Å: Chain A: M.583, I.587, L.590, S.632, L.633, Y.634, C.637, F.641 Chain B: K.659, A.660, I.663, I.664, L.667, A.668, L.672 Chain D: Y.456 Ligands: POV.4, POV.10, POV.12 Ligand excluded by PLIP POV.3: 20 residues within 4Å: Chain A: N.440, V.443, L.446, Y.447, I.450, F.475, T.478, L.482, L.485, G.486, V.488, Y.489, F.490, F.492, R.493, E.515, F.518, Y.556, Y.557 Ligands: POV.6 Ligand excluded by PLIP POV.4: 14 residues within 4Å: Chain A: H.413, V.510, K.573, L.576, R.577, C.580, M.583, I.587, E.695 Chain D: M.564 Ligands: POV.1, 8IJ.2, POV.10, POV.40 Ligand excluded by PLIP POV.6: 14 residues within 4Å: Chain A: L.446, I.449, I.450, M.453, A.454, Y.457, K.470, G.472, D.473, F.475, R.476 Ligands: POV.3, POV.7, POV.13 Ligand excluded by PLIP POV.7: 19 residues within 4Å: Chain A: Q.426, Y.438, F.441, L.442, C.445, L.446, I.449, W.551, M.554, G.560, F.561, Q.562, Q.563, M.564, W.700, R.704 Ligands: POV.6, POV.13, POV.17 Ligand excluded by PLIP POV.8: 14 residues within 4Å: Chain A: F.519, L.520, L.523, F.524, L.526, A.527, L.531, L.536, E.538, A.541, S.542, F.545 Ligands: 8IJ.2, POV.12 Ligand excluded by PLIP POV.9: 13 residues within 4Å: Chain A: D.657, F.658, K.659, A.660, V.661, I.664 Chain D: L.520, F.524, F.545, L.549 Ligands: POV.34, 8IJ.35, POV.41 Ligand excluded by PLIP POV.10: 15 residues within 4Å: Chain A: F.584, I.587, V.588, L.590, F.591, L.633 Chain D: I.449, T.452, M.453, Y.456, Y.457 Ligands: POV.1, POV.4, POV.39, POV.40 Ligand excluded by PLIP POV.12: 12 residues within 4Å: Chain A: L.520, F.524, F.545, L.549 Chain B: D.657, F.658, K.659, A.660, V.661 Ligands: POV.1, 8IJ.2, POV.8 Ligand excluded by PLIP POV.13: 15 residues within 4Å: Chain A: I.449, T.452, M.453, Y.456, Y.457, W.551 Chain B: F.584, I.587, V.588, F.591, L.633 Ligands: POV.6, POV.7, POV.14, POV.17 Ligand excluded by PLIP POV.14: 18 residues within 4Å: Chain A: Y.456 Chain B: M.583, I.587, S.632, L.633, Y.634, C.637, F.641 Chain C: K.659, A.660, I.663, I.664, L.667, A.668, L.672 Ligands: POV.13, POV.17, POV.23 Ligand excluded by PLIP POV.16: 20 residues within 4Å: Chain B: N.440, V.443, L.446, Y.447, I.450, F.475, T.478, L.482, L.485, G.486, V.488, Y.489, F.490, F.492, R.493, E.515, F.518, Y.556, Y.557 Ligands: POV.20 Ligand excluded by PLIP POV.17: 16 residues within 4Å: Chain A: Q.563, M.564 Chain B: H.413, V.510, K.573, L.576, R.577, C.580, R.581, M.583, I.587, E.695 Ligands: POV.7, POV.13, POV.14, 8IJ.15 Ligand excluded by PLIP POV.19: 15 residues within 4Å: Chain B: I.449, T.452, M.453, Y.456, Y.457, W.551 Chain C: F.584, I.587, V.588, F.591, L.633 Ligands: POV.20, POV.21, POV.24, POV.27 Ligand excluded by PLIP POV.20: 14 residues within 4Å: Chain B: L.446, I.449, I.450, M.453, A.454, Y.457, K.470, G.472, D.473, F.475, R.476 Ligands: POV.16, POV.19, POV.21 Ligand excluded by PLIP POV.21: 18 residues within 4Å: Chain B: Q.426, Y.438, F.441, L.442, C.445, L.446, I.449, W.551, M.554, G.560, F.561, Q.562, M.564, W.700, R.704 Ligands: POV.19, POV.20, POV.27 Ligand excluded by PLIP POV.22: 15 residues within 4Å: Chain B: F.491, F.519, L.520, L.523, F.524, L.526, A.527, L.531, L.536, E.538, A.541, S.542, F.545 Ligands: 8IJ.15, POV.23 Ligand excluded by PLIP POV.23: 12 residues within 4Å: Chain B: L.520, F.524, F.545, L.549 Chain C: D.657, F.658, K.659, A.660, V.661 Ligands: POV.14, 8IJ.15, POV.22 Ligand excluded by PLIP POV.24: 18 residues within 4Å: Chain B: Y.456 Chain C: M.583, I.587, S.632, L.633, Y.634, C.637, F.641 Chain D: K.659, A.660, I.663, I.664, L.667, A.668, L.672 Ligands: POV.19, POV.27, POV.33 Ligand excluded by PLIP POV.26: 20 residues within 4Å: Chain C: N.440, V.443, L.446, Y.447, I.450, F.475, T.478, L.482, L.485, G.486, V.488, Y.489, F.490, F.492, R.493, E.515, F.518, Y.556, Y.557 Ligands: POV.30 Ligand excluded by PLIP POV.27: 17 residues within 4Å: Chain B: Q.563, M.564 Chain C: H.413, V.510, K.573, L.576, R.577, L.579, C.580, R.581, M.583, I.587, E.695 Ligands: POV.19, POV.21, POV.24, 8IJ.25 Ligand excluded by PLIP POV.29: 15 residues within 4Å: Chain C: I.449, T.452, M.453, Y.456, Y.457, W.551 Chain D: F.584, I.587, V.588, F.591, L.633 Ligands: POV.30, POV.31, POV.34, POV.37 Ligand excluded by PLIP POV.30: 14 residues within 4Å: Chain C: L.446, I.449, I.450, M.453, A.454, Y.457, K.470, G.472, D.473, F.475, R.476 Ligands: POV.26, POV.29, POV.31 Ligand excluded by PLIP POV.31: 18 residues within 4Å: Chain C: Q.426, Y.438, F.441, L.442, C.445, L.446, I.449, W.551, M.554, G.560, F.561, Q.562, M.564, W.700, R.704 Ligands: POV.29, POV.30, POV.37 Ligand excluded by PLIP POV.32: 15 residues within 4Å: Chain C: F.491, F.519, L.520, L.523, F.524, L.526, A.527, L.531, L.536, E.538, A.541, S.542, F.545 Ligands: 8IJ.25, POV.33 Ligand excluded by PLIP POV.33: 12 residues within 4Å: Chain C: L.520, F.524, F.545, L.549 Chain D: D.657, F.658, K.659, A.660, V.661 Ligands: POV.24, 8IJ.25, POV.32 Ligand excluded by PLIP POV.34: 19 residues within 4Å: Chain A: K.659, A.660, I.663, I.664, L.667, A.668, I.671, L.672 Chain C: Y.456 Chain D: M.583, I.587, S.632, L.633, Y.634, C.637, F.641 Ligands: POV.9, POV.29, POV.37 Ligand excluded by PLIP POV.36: 20 residues within 4Å: Chain D: N.440, V.443, L.446, Y.447, I.450, F.475, T.478, L.482, L.485, G.486, V.488, Y.489, F.490, F.492, R.493, E.515, F.518, Y.556, Y.557 Ligands: POV.39 Ligand excluded by PLIP POV.37: 17 residues within 4Å: Chain C: Q.563, M.564 Chain D: H.413, V.510, K.573, L.576, R.577, L.579, C.580, R.581, M.583, I.587, E.695 Ligands: POV.29, POV.31, POV.34, 8IJ.35 Ligand excluded by PLIP POV.39: 13 residues within 4Å: Chain D: I.449, I.450, M.453, A.454, Y.457, K.470, G.472, D.473, F.475, R.476 Ligands: POV.10, POV.36, POV.40 Ligand excluded by PLIP POV.40: 19 residues within 4Å: Chain A: F.584 Chain D: Q.426, Y.438, F.441, L.442, C.445, L.446, I.449, W.551, M.554, G.560, F.561, Q.562, M.564, W.700, R.704 Ligands: POV.4, POV.10, POV.39 Ligand excluded by PLIP POV.41: 14 residues within 4Å: Chain D: F.519, L.520, L.523, F.524, L.526, A.527, L.531, L.536, E.538, A.541, S.542, F.545 Ligands: POV.9, 8IJ.35 Ligand excluded by PLIP

4 x 8IJ: (2R)-3-{[(R)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctadecanoate(Non-covalent)

8IJ.2: 30 residues within 4Å: Chain A: R.412, H.413, D.511, S.512, Y.513, S.514, M.516, L.517, L.520, F.545, A.548, L.549, T.552, N.553, L.555, Y.556, R.559, E.572, I.575, L.576, I.699, L.702, Q.703, I.706 Chain B: F.593, I.664, L.672 Ligands: POV.4, POV.8, POV.12 24 PLIP interactions: 20 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.513, A:M.516, A:L.517, A:L.520, A:F.545, A:A.548, A:L.549, A:T.552, A:L.555, A:L.555, A:Y.556, A:L.576, B:F.593, B:F.593, B:I.664, B:L.672 Hydrogen bonds: A:R.412, A:R.412, A:V.510, A:Y.513, A:S.514, A:E.572, A:Q.703 Salt bridges: A:R.559 8IJ.15: 30 residues within 4Å: Chain B: R.412, H.413, D.511, S.512, Y.513, S.514, M.516, L.517, L.520, F.545, A.548, L.549, T.552, N.553, L.555, Y.556, R.559, E.572, I.575, L.576, I.699, L.702, Q.703, I.706 Chain C: F.593, I.664, L.672 Ligands: POV.17, POV.22, POV.23 26 PLIP interactions: 4 interactions with chain C, 22 interactions with chain B Hydrophobic interactions: C:F.593, C:F.593, C:I.664, C:L.672, B:Y.513, B:M.516, B:L.517, B:L.520, B:F.545, B:A.548, B:L.549, B:T.552, B:L.555, B:L.555, B:Y.556, B:L.576 Hydrogen bonds: B:R.412, B:R.412, B:H.413, B:Y.513, B:S.514, B:S.514, B:E.572, B:E.572, B:Q.703 Salt bridges: B:R.559 8IJ.25: 30 residues within 4Å: Chain C: R.412, H.413, D.511, S.512, Y.513, S.514, M.516, L.517, L.520, F.545, A.548, L.549, T.552, N.553, L.555, Y.556, R.559, E.572, I.575, L.576, I.699, L.702, Q.703, I.706 Chain D: F.593, I.664, L.672 Ligands: POV.27, POV.32, POV.33 26 PLIP interactions: 22 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:Y.513, C:M.516, C:L.517, C:L.520, C:F.545, C:A.548, C:L.549, C:T.552, C:L.555, C:L.555, C:Y.556, C:L.576, D:F.593, D:F.593, D:I.664, D:L.672 Hydrogen bonds: C:R.412, C:R.412, C:H.413, C:Y.513, C:S.514, C:S.514, C:E.572, C:E.572, C:Q.703 Salt bridges: C:R.559 8IJ.35: 30 residues within 4Å: Chain A: F.593, I.664, L.672 Chain D: R.412, H.413, D.511, S.512, Y.513, S.514, M.516, L.517, L.520, F.545, A.548, L.549, T.552, N.553, L.555, Y.556, R.559, E.572, I.575, L.576, I.699, L.702, Q.703, I.706 Ligands: POV.9, POV.37, POV.41 21 PLIP interactions: 19 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:Y.513, D:M.516, D:L.520, D:F.545, D:A.548, D:T.552, D:L.555, D:L.555, D:Y.556, D:L.576, A:F.593, A:I.664 Hydrogen bonds: D:R.412, D:R.412, D:Y.513, D:S.514, D:S.514, D:E.572, D:E.572, D:Q.703 Salt bridges: D:R.559

4 x TRD: TRIDECANE(Non-covalent)

TRD.5: 12 residues within 4Å: Chain A: F.451, A.454, A.455, E.480, I.481, S.483, V.484, T.528, V.529, Y.532, F.533, M.543 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.451, A:F.451, A:A.454, A:E.480, A:E.480, A:I.481, A:V.484, A:T.528, A:V.529, A:Y.532, A:Y.532, A:F.533, A:F.533 TRD.18: 11 residues within 4Å: Chain B: F.451, A.454, E.480, I.481, S.483, V.484, T.528, V.529, Y.532, F.533, M.543 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.451, B:A.454, B:E.480, B:I.481, B:V.484, B:T.528, B:V.529, B:Y.532, B:Y.532, B:F.533, B:F.533 TRD.28: 11 residues within 4Å: Chain C: F.451, A.454, E.480, I.481, S.483, V.484, T.528, V.529, Y.532, F.533, M.543 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:F.451, C:A.454, C:E.480, C:E.480, C:I.481, C:V.484, C:T.528, C:V.529, C:Y.532, C:Y.532, C:F.533, C:F.533 TRD.38: 12 residues within 4Å: Chain D: F.451, A.454, A.455, E.480, I.481, S.483, V.484, T.528, V.529, Y.532, F.533, M.543 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:F.451, D:F.451, D:A.454, D:E.480, D:E.480, D:I.481, D:V.484, D:T.528, D:V.529, D:Y.532, D:Y.532, D:F.533, D:F.533

2 x NA: SODIUM ION(Non-functional Binders)

NA.11: 6 residues within 4Å: Chain A: G.646 Chain B: G.646 Chain C: G.646 Chain D: G.646, M.647 Ligands: NA.42 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.646 NA.42: 1 residues within 4Å: Ligands: NA.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sanchez-Hernandez, R. et al., Structural basis of the inhibition of TRPV1 by analgesic sesquiterpenes. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-07-23

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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