SMTL ID : 8gf9.1

Cryo-EM structure of human TRPV1 in cNW11 nanodisc and POPC:POPE:POPG lipids

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

POV.1: 26 residues within 4Å: Chain A: I.575, L.579, M.583, Y.586, I.587, L.590, S.632, L.633, Y.634, S.635, C.637, L.638, F.641 Chain B: K.659, A.660, I.663, I.664, L.667, A.668, I.671, L.672, L.676 Ligands: 8IJ.2, POV.13, POV.33, POV.39 Ligand excluded by PLIP POV.3: 20 residues within 4Å: Chain A: F.439, N.440, L.442, V.443, Y.444, L.446, Y.447, I.450, L.482, L.485, G.486, Y.489, F.490, R.493, S.514, E.515, F.518, Y.556, Y.557 Ligands: POV.6 Ligand excluded by PLIP POV.4: 15 residues within 4Å: Chain A: F.451, A.454, A.455, V.477, G.479, E.480, I.481, S.483, V.484, T.528, V.529, Y.532, F.533, Y.539, M.543 Ligand excluded by PLIP POV.5: 22 residues within 4Å: Chain A: I.449, T.452, M.453, Y.456, Y.457, W.551, M.554 Chain B: F.584, I.587, V.588, L.590, F.591, T.595, N.631, S.632, L.633, C.637 Ligands: POV.6, POV.7, POV.9, POV.14, POV.23 Ligand excluded by PLIP POV.6: 19 residues within 4Å: Chain A: L.446, I.449, I.450, M.453, A.454, Y.457, R.458, P.459, K.470, G.472, D.473, F.475, R.476, T.478, G.479, L.482 Ligands: POV.3, POV.5, POV.7 Ligand excluded by PLIP POV.7: 22 residues within 4Å: Chain A: Q.426, W.429, K.434, Y.438, F.441, L.442, C.445, L.446, I.449, W.551, M.554, T.558, F.561, Q.562, Q.563, M.564, W.700, R.704 Chain B: F.584 Ligands: POV.5, POV.6, POV.9 Ligand excluded by PLIP POV.8: 21 residues within 4Å: Chain A: F.491, I.495, L.508, F.509, M.516, F.519, L.520, L.523, F.524, L.526, A.527, V.530, L.531, L.536, E.538, A.541, S.542, F.545 Chain B: F.658 Ligands: 8IJ.2, POV.13 Ligand excluded by PLIP POV.9: 19 residues within 4Å: Chain A: Q.563, M.564 Chain B: V.510, Y.513, I.575, L.576, R.577, L.579, C.580, R.581, M.583, F.584, I.587 Chain C: I.671 Ligands: POV.5, POV.7, POV.14, 8IJ.15, POV.23 Ligand excluded by PLIP POV.10: 18 residues within 4Å: Chain A: Y.656, F.658, K.659, A.660, V.661, I.664 Chain D: L.517, L.520, F.524, E.538, A.541, F.545, L.549 Ligands: POV.28, POV.32, POV.35, 8IJ.36, POV.42 Ligand excluded by PLIP POV.13: 18 residues within 4Å: Chain A: L.517, L.520, F.524, E.538, A.541, F.545, L.549 Chain B: Y.656, F.658, K.659, A.660, V.661, I.664 Ligands: POV.1, 8IJ.2, POV.8, POV.33, POV.39 Ligand excluded by PLIP POV.14: 26 residues within 4Å: Chain B: I.575, L.579, M.583, Y.586, I.587, L.590, S.632, L.633, Y.634, S.635, C.637, L.638, F.641 Chain C: K.659, A.660, I.663, I.664, L.667, A.668, I.671, L.672, L.676 Ligands: POV.5, POV.9, 8IJ.15, POV.23 Ligand excluded by PLIP POV.16: 20 residues within 4Å: Chain B: F.439, N.440, L.442, V.443, Y.444, L.446, Y.447, I.450, L.482, L.485, G.486, Y.489, F.490, R.493, S.514, E.515, F.518, Y.556, Y.557 Ligands: POV.19 Ligand excluded by PLIP POV.17: 15 residues within 4Å: Chain B: F.451, A.454, A.455, V.477, G.479, E.480, I.481, S.483, V.484, T.528, V.529, Y.532, F.533, Y.539, M.543 Ligand excluded by PLIP POV.18: 22 residues within 4Å: Chain B: I.449, T.452, M.453, Y.456, Y.457, W.551, M.554 Chain C: F.584, I.587, V.588, L.590, F.591, T.595, N.631, S.632, L.633, C.637 Ligands: POV.19, POV.20, POV.22, POV.24, POV.34 Ligand excluded by PLIP POV.19: 19 residues within 4Å: Chain B: L.446, I.449, I.450, M.453, A.454, Y.457, R.458, P.459, K.470, G.472, D.473, F.475, R.476, T.478, G.479, L.482 Ligands: POV.16, POV.18, POV.20 Ligand excluded by PLIP POV.20: 22 residues within 4Å: Chain B: Q.426, W.429, K.434, Y.438, F.441, L.442, C.445, L.446, I.449, W.551, M.554, T.558, F.561, Q.562, Q.563, M.564, W.700, R.704 Chain C: F.584 Ligands: POV.18, POV.19, POV.22 Ligand excluded by PLIP POV.21: 21 residues within 4Å: Chain B: F.491, I.495, L.508, F.509, M.516, F.519, L.520, L.523, F.524, L.526, A.527, V.530, L.531, L.536, E.538, A.541, S.542, F.545 Chain C: F.658 Ligands: 8IJ.15, POV.23 Ligand excluded by PLIP POV.22: 19 residues within 4Å: Chain B: Q.563, M.564 Chain C: V.510, Y.513, I.575, L.576, R.577, L.579, C.580, R.581, M.583, F.584, I.587 Chain D: I.671 Ligands: POV.18, POV.20, POV.24, 8IJ.25, POV.34 Ligand excluded by PLIP POV.23: 18 residues within 4Å: Chain B: L.517, L.520, F.524, E.538, A.541, F.545, L.549 Chain C: Y.656, F.658, K.659, A.660, V.661, I.664 Ligands: POV.5, POV.9, POV.14, 8IJ.15, POV.21 Ligand excluded by PLIP POV.24: 26 residues within 4Å: Chain C: I.575, L.579, M.583, Y.586, I.587, L.590, S.632, L.633, Y.634, S.635, C.637, L.638, F.641 Chain D: K.659, A.660, I.663, I.664, L.667, A.668, I.671, L.672, L.676 Ligands: POV.18, POV.22, 8IJ.25, POV.34 Ligand excluded by PLIP POV.26: 20 residues within 4Å: Chain C: F.439, N.440, L.442, V.443, Y.444, L.446, Y.447, I.450, L.482, L.485, G.486, Y.489, F.490, R.493, S.514, E.515, F.518, Y.556, Y.557 Ligands: POV.29 Ligand excluded by PLIP POV.27: 15 residues within 4Å: Chain C: F.451, A.454, A.455, V.477, G.479, E.480, I.481, S.483, V.484, T.528, V.529, Y.532, F.533, Y.539, M.543 Ligand excluded by PLIP POV.28: 22 residues within 4Å: Chain C: I.449, T.452, M.453, Y.456, Y.457, W.551, M.554 Chain D: F.584, I.587, V.588, L.590, F.591, T.595, N.631, S.632, L.633, C.637 Ligands: POV.10, POV.29, POV.30, POV.32, POV.35 Ligand excluded by PLIP POV.29: 19 residues within 4Å: Chain C: L.446, I.449, I.450, M.453, A.454, Y.457, R.458, P.459, K.470, G.472, D.473, F.475, R.476, T.478, G.479, L.482 Ligands: POV.26, POV.28, POV.30 Ligand excluded by PLIP POV.30: 22 residues within 4Å: Chain C: Q.426, W.429, K.434, Y.438, F.441, L.442, C.445, L.446, I.449, W.551, M.554, T.558, F.561, Q.562, Q.563, M.564, W.700, R.704 Chain D: F.584 Ligands: POV.28, POV.29, POV.32 Ligand excluded by PLIP POV.31: 21 residues within 4Å: Chain C: F.491, I.495, L.508, F.509, M.516, F.519, L.520, L.523, F.524, L.526, A.527, V.530, L.531, L.536, E.538, A.541, S.542, F.545 Chain D: F.658 Ligands: 8IJ.25, POV.34 Ligand excluded by PLIP POV.32: 19 residues within 4Å: Chain A: I.671 Chain C: Q.563, M.564 Chain D: V.510, Y.513, I.575, L.576, R.577, L.579, C.580, R.581, M.583, F.584, I.587 Ligands: POV.10, POV.28, POV.30, POV.35, 8IJ.36 Ligand excluded by PLIP POV.33: 19 residues within 4Å: Chain A: V.510, Y.513, I.575, L.576, R.577, L.579, C.580, R.581, M.583, F.584, I.587 Chain B: I.671 Chain D: Q.563, M.564 Ligands: POV.1, 8IJ.2, POV.13, POV.39, POV.41 Ligand excluded by PLIP POV.34: 18 residues within 4Å: Chain C: L.517, L.520, F.524, E.538, A.541, F.545, L.549 Chain D: Y.656, F.658, K.659, A.660, V.661, I.664 Ligands: POV.18, POV.22, POV.24, 8IJ.25, POV.31 Ligand excluded by PLIP POV.35: 26 residues within 4Å: Chain A: K.659, A.660, I.663, I.664, L.667, A.668, I.671, L.672, L.676 Chain D: I.575, L.579, M.583, Y.586, I.587, L.590, S.632, L.633, Y.634, S.635, C.637, L.638, F.641 Ligands: POV.10, POV.28, POV.32, 8IJ.36 Ligand excluded by PLIP POV.37: 20 residues within 4Å: Chain D: F.439, N.440, L.442, V.443, Y.444, L.446, Y.447, I.450, L.482, L.485, G.486, Y.489, F.490, R.493, S.514, E.515, F.518, Y.556, Y.557 Ligands: POV.40 Ligand excluded by PLIP POV.38: 15 residues within 4Å: Chain D: F.451, A.454, A.455, V.477, G.479, E.480, I.481, S.483, V.484, T.528, V.529, Y.532, F.533, Y.539, M.543 Ligand excluded by PLIP POV.39: 22 residues within 4Å: Chain A: F.584, I.587, V.588, L.590, F.591, T.595, N.631, S.632, L.633, C.637 Chain D: I.449, T.452, M.453, Y.456, Y.457, W.551, M.554 Ligands: POV.1, POV.13, POV.33, POV.40, POV.41 Ligand excluded by PLIP POV.40: 19 residues within 4Å: Chain D: L.446, I.449, I.450, M.453, A.454, Y.457, R.458, P.459, K.470, G.472, D.473, F.475, R.476, T.478, G.479, L.482 Ligands: POV.37, POV.39, POV.41 Ligand excluded by PLIP POV.41: 22 residues within 4Å: Chain A: F.584 Chain D: Q.426, W.429, K.434, Y.438, F.441, L.442, C.445, L.446, I.449, W.551, M.554, T.558, F.561, Q.562, Q.563, M.564, W.700, R.704 Ligands: POV.33, POV.39, POV.40 Ligand excluded by PLIP POV.42: 21 residues within 4Å: Chain A: F.658 Chain D: F.491, I.495, L.508, F.509, M.516, F.519, L.520, L.523, F.524, L.526, A.527, V.530, L.531, L.536, E.538, A.541, S.542, F.545 Ligands: POV.10, 8IJ.36 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: 39 residues within 4Å: Chain A: R.412, H.413, F.509, D.511, S.512, Y.513, S.514, M.516, L.517, F.518, L.520, F.524, F.545, A.548, L.549, T.552, N.553, L.555, Y.556, R.559, I.571, E.572, K.573, I.575, L.576, I.699, L.702, Q.703, I.706 Chain B: F.589, F.593, I.664, L.665, A.668, L.672 Ligands: POV.1, POV.8, POV.13, POV.33 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:M.516, A:L.517, A:L.520, A:F.545, A:L.549, A:L.555, A:L.555, A:I.575, A:I.575, B:F.593, B:A.668 Hydrogen bonds: A:R.412, A:R.412, A:D.511, A:D.511, A:Y.513, A:S.514, A:E.572, A:E.572, A:Q.703 Salt bridges: A:R.559 8IJ.15: 39 residues within 4Å: Chain B: R.412, H.413, F.509, D.511, S.512, Y.513, S.514, M.516, L.517, F.518, L.520, F.524, F.545, A.548, L.549, T.552, N.553, L.555, Y.556, R.559, I.571, E.572, K.573, I.575, L.576, I.699, L.702, Q.703, I.706 Chain C: F.589, F.593, I.664, L.665, A.668, L.672 Ligands: POV.9, POV.14, POV.21, POV.23 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:M.516, B:L.517, B:L.520, B:F.545, B:L.549, B:L.555, B:L.555, B:I.575, B:I.575, C:F.593, C:A.668 Hydrogen bonds: B:R.412, B:R.412, B:D.511, B:D.511, B:Y.513, B:S.514, B:E.572, B:E.572, B:Q.703 Salt bridges: B:R.559 8IJ.25: 39 residues within 4Å: Chain C: R.412, H.413, F.509, D.511, S.512, Y.513, S.514, M.516, L.517, F.518, L.520, F.524, F.545, A.548, L.549, T.552, N.553, L.555, Y.556, R.559, I.571, E.572, K.573, I.575, L.576, I.699, L.702, Q.703, I.706 Chain D: F.589, F.593, I.664, L.665, A.668, L.672 Ligands: POV.22, POV.24, POV.31, POV.34 20 PLIP interactions: 19 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:M.516, C:L.517, C:L.520, C:F.545, C:L.549, C:L.555, C:L.555, C:I.575, C:I.575, D:F.593 Hydrogen bonds: C:R.412, C:R.412, C:D.511, C:D.511, C:Y.513, C:S.514, C:E.572, C:E.572, C:Q.703 Salt bridges: C:R.559 8IJ.36: 39 residues within 4Å: Chain A: F.589, F.593, I.664, L.665, A.668, L.672 Chain D: R.412, H.413, F.509, D.511, S.512, Y.513, S.514, M.516, L.517, F.518, L.520, F.524, F.545, A.548, L.549, T.552, N.553, L.555, Y.556, R.559, I.571, E.572, K.573, I.575, L.576, I.699, L.702, Q.703, I.706 Ligands: POV.10, POV.32, POV.35, POV.42 21 PLIP interactions: 19 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:M.516, D:L.517, D:L.520, D:F.545, D:L.549, D:L.555, D:L.555, D:I.575, D:I.575, A:F.593, A:A.668 Hydrogen bonds: D:R.412, D:R.412, D:D.511, D:D.511, D:Y.513, D:S.514, D:E.572, D:E.572, D:Q.703 Salt bridges: D:R.559

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

NA.11: 8 residues within 4Å: Chain A: G.646, M.647 Chain B: G.646, M.647 Chain C: G.646, M.647 Chain D: G.646, M.647 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.646 NA.12: 4 residues within 4Å: Chain A: G.646 Chain B: G.646 Chain C: G.646 Chain D: G.646 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neuberger, A. et al., Human TRPV1 structure and inhibition by the analgesic SB-366791. Nat Commun (2023)

Release Date

2023-05-10

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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