SMTL ID : 8gf8.1

Cryo-EM structure of human TRPV1 in cNW11 nanodisc and soybean 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: 25 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 Chain D: Y.456 Ligands: 8IJ.2, POV.10, POV.13 Ligand excluded by PLIP POV.3: 21 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, D.710 Ligands: POV.6 Ligand excluded by PLIP POV.4: 17 residues within 4Å: Chain A: K.506, F.509, V.510, Y.513, L.576, R.577, C.580, R.581, M.583, F.584, I.587, K.691 Chain D: Q.563, M.564 Ligands: POV.10, POV.13, POV.41 Ligand excluded by PLIP POV.5: 13 residues within 4Å: Chain A: F.451, A.454, A.455, E.480, I.481, S.483, V.484, M.525, T.528, V.529, Y.532, F.533, M.543 Ligand excluded by PLIP POV.6: 16 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, T.478, G.479, L.482 Ligands: POV.3, POV.14 Ligand excluded by PLIP POV.7: 24 residues within 4Å: Chain A: Q.426, W.429, D.430, Y.438, F.441, L.442, C.445, I.449, W.551, M.554, L.555, Y.557, T.558, G.560, F.561, Q.562, Q.563, M.564, W.700, R.704 Chain B: F.584, V.588 Ligands: POV.14, POV.19 Ligand excluded by PLIP POV.8: 18 residues within 4Å: Chain A: F.491, F.519, L.520, S.522, L.523, F.524, L.526, A.527, V.530, L.531, S.534, L.536, E.538, A.541, S.542, F.545 Ligands: 8IJ.2, POV.13 Ligand excluded by PLIP POV.9: 19 residues within 4Å: Chain A: Y.656, D.657, 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.31, POV.35, 8IJ.36, POV.38, POV.42 Ligand excluded by PLIP POV.10: 19 residues within 4Å: Chain A: F.584, I.587, V.588, L.590, F.591, T.595, L.633, C.637 Chain D: I.449, T.452, M.453, Y.456, Y.457, W.551 Ligands: POV.1, POV.4, POV.13, POV.40, POV.41 Ligand excluded by PLIP POV.13: 19 residues within 4Å: Chain A: L.517, L.520, F.524, E.538, A.541, F.545, L.549 Chain B: Y.656, D.657, F.658, K.659, A.660, V.661, I.664 Ligands: POV.1, 8IJ.2, POV.4, POV.8, POV.10 Ligand excluded by PLIP POV.14: 19 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, L.590, F.591, T.595, L.633, C.637 Ligands: POV.6, POV.7, POV.15, POV.16, POV.19 Ligand excluded by PLIP POV.15: 19 residues within 4Å: Chain B: L.517, L.520, F.524, E.538, A.541, F.545, L.549 Chain C: Y.656, D.657, F.658, K.659, A.660, V.661, I.664 Ligands: POV.14, POV.16, 8IJ.17, POV.19, POV.24 Ligand excluded by PLIP POV.16: 25 residues within 4Å: Chain A: Y.456 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 Ligands: POV.14, POV.15, 8IJ.17 Ligand excluded by PLIP POV.18: 21 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, D.710 Ligands: POV.22 Ligand excluded by PLIP POV.19: 17 residues within 4Å: Chain A: Q.563, M.564 Chain B: K.506, F.509, V.510, Y.513, L.576, R.577, C.580, R.581, M.583, F.584, I.587, K.691 Ligands: POV.7, POV.14, POV.15 Ligand excluded by PLIP POV.20: 13 residues within 4Å: Chain B: F.451, A.454, A.455, E.480, I.481, S.483, V.484, M.525, T.528, V.529, Y.532, F.533, M.543 Ligand excluded by PLIP POV.21: 19 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, L.590, F.591, T.595, L.633, C.637 Ligands: POV.22, POV.23, POV.25, POV.26, POV.29 Ligand excluded by PLIP POV.22: 16 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, T.478, G.479, L.482 Ligands: POV.18, POV.21 Ligand excluded by PLIP POV.23: 24 residues within 4Å: Chain B: Q.426, W.429, D.430, Y.438, F.441, L.442, C.445, I.449, W.551, M.554, L.555, Y.557, T.558, G.560, F.561, Q.562, Q.563, M.564, W.700, R.704 Chain C: F.584, V.588 Ligands: POV.21, POV.29 Ligand excluded by PLIP POV.24: 18 residues within 4Å: Chain B: F.491, F.519, L.520, S.522, L.523, F.524, L.526, A.527, V.530, L.531, S.534, L.536, E.538, A.541, S.542, F.545 Ligands: POV.15, 8IJ.17 Ligand excluded by PLIP POV.25: 19 residues within 4Å: Chain C: L.517, L.520, F.524, E.538, A.541, F.545, L.549 Chain D: Y.656, D.657, F.658, K.659, A.660, V.661, I.664 Ligands: POV.21, POV.26, 8IJ.27, POV.29, POV.34 Ligand excluded by PLIP POV.26: 25 residues within 4Å: Chain B: Y.456 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 Ligands: POV.21, POV.25, 8IJ.27 Ligand excluded by PLIP POV.28: 21 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, D.710 Ligands: POV.32 Ligand excluded by PLIP POV.29: 17 residues within 4Å: Chain B: Q.563, M.564 Chain C: K.506, F.509, V.510, Y.513, L.576, R.577, C.580, R.581, M.583, F.584, I.587, K.691 Ligands: POV.21, POV.23, POV.25 Ligand excluded by PLIP POV.30: 13 residues within 4Å: Chain C: F.451, A.454, A.455, E.480, I.481, S.483, V.484, M.525, T.528, V.529, Y.532, F.533, M.543 Ligand excluded by PLIP POV.31: 19 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, L.590, F.591, T.595, L.633, C.637 Ligands: POV.9, POV.32, POV.33, POV.35, POV.38 Ligand excluded by PLIP POV.32: 16 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, T.478, G.479, L.482 Ligands: POV.28, POV.31 Ligand excluded by PLIP POV.33: 24 residues within 4Å: Chain C: Q.426, W.429, D.430, Y.438, F.441, L.442, C.445, I.449, W.551, M.554, L.555, Y.557, T.558, G.560, F.561, Q.562, Q.563, M.564, W.700, R.704 Chain D: F.584, V.588 Ligands: POV.31, POV.38 Ligand excluded by PLIP POV.34: 19 residues within 4Å: Chain C: F.491, I.495, F.519, L.520, S.522, L.523, F.524, L.526, A.527, V.530, L.531, S.534, L.536, E.538, A.541, S.542, F.545 Ligands: POV.25, 8IJ.27 Ligand excluded by PLIP POV.35: 25 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: 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.9, POV.31, 8IJ.36 Ligand excluded by PLIP POV.37: 21 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, D.710 Ligands: POV.40 Ligand excluded by PLIP POV.38: 17 residues within 4Å: Chain C: Q.563, M.564 Chain D: K.506, F.509, V.510, Y.513, L.576, R.577, C.580, R.581, M.583, F.584, I.587, K.691 Ligands: POV.9, POV.31, POV.33 Ligand excluded by PLIP POV.39: 13 residues within 4Å: Chain D: F.451, A.454, A.455, E.480, I.481, S.483, V.484, M.525, T.528, V.529, Y.532, F.533, M.543 Ligand excluded by PLIP POV.40: 16 residues within 4Å: Chain D: L.446, I.449, I.450, M.453, A.454, Y.457, K.470, G.472, D.473, F.475, R.476, T.478, G.479, L.482 Ligands: POV.10, POV.37 Ligand excluded by PLIP POV.41: 24 residues within 4Å: Chain A: F.584, V.588 Chain D: Q.426, W.429, D.430, Y.438, F.441, L.442, C.445, I.449, W.551, M.554, L.555, Y.557, T.558, G.560, F.561, Q.562, Q.563, M.564, W.700, R.704 Ligands: POV.4, POV.10 Ligand excluded by PLIP POV.42: 18 residues within 4Å: Chain D: F.491, F.519, L.520, S.522, L.523, F.524, L.526, A.527, V.530, L.531, S.534, L.536, E.538, A.541, S.542, F.545 Ligands: POV.9, 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: 36 residues within 4Å: Chain A: H.413, 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 28 PLIP interactions: 25 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.513, A:M.516, A:L.517, A:L.517, A:L.520, A:F.524, A:F.545, A:F.545, A:A.548, A:L.549, A:L.555, A:L.555, A:Y.556, A:I.575, A:I.575, B:F.593, B:I.664, B:A.668 Hydrogen bonds: A:D.511, A:D.511, A:Y.513, A:S.514, A:E.572, A:E.572, A:K.573, A:Q.703 Salt bridges: A:R.559, A:R.559 8IJ.17: 36 residues within 4Å: Chain B: H.413, 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.15, POV.16, POV.24 27 PLIP interactions: 25 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:Y.513, B:M.516, B:L.517, B:L.517, B:L.520, B:F.524, B:F.545, B:F.545, B:A.548, B:L.549, B:L.555, B:L.555, B:Y.556, B:I.575, B:I.575, C:F.593, C:I.664 Hydrogen bonds: B:D.511, B:D.511, B:Y.513, B:S.514, B:E.572, B:E.572, B:K.573, B:Q.703 Salt bridges: B:R.559, B:R.559 8IJ.27: 36 residues within 4Å: Chain C: H.413, 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.25, POV.26, POV.34 28 PLIP interactions: 25 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:Y.513, C:M.516, C:L.517, C:L.517, C:L.520, C:F.524, C:F.545, C:F.545, C:A.548, C:L.549, C:L.555, C:L.555, C:Y.556, C:I.575, C:I.575, D:F.593, D:I.664, D:A.668 Hydrogen bonds: C:D.511, C:D.511, C:Y.513, C:S.514, C:E.572, C:E.572, C:K.573, C:Q.703 Salt bridges: C:R.559, C:R.559 8IJ.36: 36 residues within 4Å: Chain A: F.589, F.593, I.664, L.665, A.668, L.672 Chain D: H.413, 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.9, POV.35, POV.42 28 PLIP interactions: 25 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:Y.513, D:M.516, D:L.517, D:L.517, D:L.520, D:F.524, D:F.545, D:F.545, D:A.548, D:L.549, D:L.555, D:L.555, D:Y.556, D:I.575, D:I.575, A:F.593, A:I.664, A:A.668 Hydrogen bonds: D:D.511, D:D.511, D:Y.513, D:S.514, D:E.572, D:E.572, D:K.573, D:Q.703 Salt bridges: D:R.559, D:R.559

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

NA.11: 5 residues within 4Å: Chain A: G.646 Chain B: G.646 Chain C: G.646 Chain D: G.646 Ligands: NA.12 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.646 NA.12: 5 residues within 4Å: Chain A: G.646 Chain B: G.646 Chain C: G.646 Chain D: G.646 Ligands: NA.11 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.
Show / Hide

Transient receptor potential cation channel subfamily V member 1

Related Entries With Identical Sequence