SMTL ID : 7ugg.1

Cryo-EM structure of TRPV3 in complex with the anesthetic dyclonine

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

POV.1: 14 residues within 4Å: Chain A: F.592, L.599, V.603, F.625, S.626 Chain B: F.449, I.453, L.457, Y.460, Y.461, W.559 Ligands: POV.3, N8R.5, POV.10 Ligand excluded by PLIP POV.2: 16 residues within 4Å: Chain A: Y.439, M.440, S.444, W.493, C.496, I.497, K.500, E.501, F.522, H.523, F.526, Y.564, Y.565, M.706, P.708, L.711 Ligand excluded by PLIP POV.3: 10 residues within 4Å: Chain A: L.517, L.584, H.585, L.588, K.589, L.591, F.592 Chain B: S.571 Ligands: POV.1, POV.4 Ligand excluded by PLIP POV.4: 21 residues within 4Å: Chain A: L.517, S.518, W.521, F.522, L.553, A.556, L.557, A.560, L.563, R.567, S.576, V.577, Q.580, I.583, L.584, L.588, Q.695 Chain D: F.601, F.656 Ligands: POV.3, POV.23 Ligand excluded by PLIP POV.6: 12 residues within 4Å: Chain A: S.607, L.608, T.649, Y.650, L.653, F.656 Chain B: K.545, E.546, L.548, A.549, L.553 Ligands: POV.14 Ligand excluded by PLIP POV.8: 13 residues within 4Å: Chain A: W.433, K.438, Y.439, F.441, F.442, L.443, F.445, F.449, Y.565, G.568, F.569 Chain D: F.592 Ligands: POV.25 Ligand excluded by PLIP POV.10: 13 residues within 4Å: Chain A: F.592 Chain B: W.433, K.438, Y.439, F.441, F.442, L.443, F.445, F.449, Y.565, G.568, F.569 Ligands: POV.1 Ligand excluded by PLIP POV.11: 14 residues within 4Å: Chain B: F.592, L.599, V.603, F.625, S.626 Chain C: F.449, I.453, L.457, Y.460, Y.461, W.559 Ligands: N8R.7, POV.13, POV.17 Ligand excluded by PLIP POV.12: 14 residues within 4Å: Chain B: Y.439, M.440, S.444, W.493, C.496, I.497, K.500, E.501, H.523, F.526, Y.564, Y.565, M.706, L.711 Ligand excluded by PLIP POV.13: 10 residues within 4Å: Chain B: L.517, L.584, H.585, L.588, K.589, L.591, F.592 Chain C: S.571 Ligands: POV.11, POV.14 Ligand excluded by PLIP POV.14: 23 residues within 4Å: Chain A: F.597, F.601, F.656, L.664 Chain B: L.517, S.518, W.521, F.522, L.553, A.556, L.557, A.560, L.563, R.567, S.576, V.577, Q.580, I.583, L.584, L.588, Q.695 Ligands: POV.6, POV.13 Ligand excluded by PLIP POV.15: 12 residues within 4Å: Chain B: S.607, L.608, T.649, Y.650, L.653, F.656 Chain C: K.545, E.546, L.548, A.549, L.553 Ligands: POV.21 Ligand excluded by PLIP POV.17: 13 residues within 4Å: Chain B: F.592 Chain C: W.433, K.438, Y.439, F.441, F.442, L.443, F.445, F.449, Y.565, G.568, F.569 Ligands: POV.11 Ligand excluded by PLIP POV.18: 13 residues within 4Å: Chain C: F.592, L.599, V.603, F.625, S.626 Chain D: I.453, L.457, Y.460, Y.461, W.559 Ligands: N8R.16, POV.20, POV.24 Ligand excluded by PLIP POV.19: 14 residues within 4Å: Chain C: Y.439, M.440, S.444, W.493, C.496, I.497, K.500, E.501, H.523, F.526, Y.564, Y.565, M.706, L.711 Ligand excluded by PLIP POV.20: 10 residues within 4Å: Chain C: L.517, L.584, H.585, L.588, K.589, L.591, F.592 Chain D: S.571 Ligands: POV.18, POV.21 Ligand excluded by PLIP POV.21: 22 residues within 4Å: Chain B: F.601, F.656, L.664 Chain C: L.517, S.518, W.521, F.522, L.553, A.556, L.557, A.560, L.563, R.567, S.576, V.577, Q.580, I.583, L.584, L.588, Q.695 Ligands: POV.15, POV.20 Ligand excluded by PLIP POV.22: 12 residues within 4Å: Chain C: S.607, L.608, T.649, Y.650, L.653, F.656 Chain D: K.545, E.546, L.548, A.549, L.553 Ligands: POV.28 Ligand excluded by PLIP POV.23: 12 residues within 4Å: Chain A: K.545, E.546, L.548, A.549, L.553 Chain D: S.607, L.608, T.649, Y.650, L.653, F.656 Ligands: POV.4 Ligand excluded by PLIP POV.24: 13 residues within 4Å: Chain C: F.592 Chain D: W.433, K.438, Y.439, F.441, F.442, L.443, F.445, F.449, Y.565, G.568, F.569 Ligands: POV.18 Ligand excluded by PLIP POV.25: 14 residues within 4Å: Chain A: F.449, I.453, L.457, Y.460, Y.461, W.559 Chain D: F.592, L.599, V.603, F.625, S.626 Ligands: POV.8, POV.27, N8R.29 Ligand excluded by PLIP POV.26: 15 residues within 4Å: Chain D: Y.439, M.440, S.444, W.493, C.496, I.497, K.500, E.501, F.522, H.523, F.526, Y.564, Y.565, M.706, L.711 Ligand excluded by PLIP POV.27: 10 residues within 4Å: Chain A: S.571 Chain D: L.517, L.584, H.585, L.588, K.589, L.591, F.592 Ligands: POV.25, POV.28 Ligand excluded by PLIP POV.28: 23 residues within 4Å: Chain C: F.597, F.601, F.656, T.660, L.664 Chain D: L.517, S.518, W.521, F.522, L.553, L.557, A.560, L.563, R.567, S.576, V.577, Q.580, I.583, L.584, L.588, Q.695 Ligands: POV.22, POV.27 Ligand excluded by PLIP

4 x N8R: Dyclonine(Non-covalent)

N8R.5: 11 residues within 4Å: Chain A: F.590, L.591, Y.594, F.633, T.636, L.670 Chain D: I.659, I.663, F.666, V.667 Ligands: POV.1 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:F.590, A:L.591, A:Y.594, A:Y.594, A:F.633, A:T.636, A:L.670, D:I.659, D:I.663, D:V.667 N8R.7: 11 residues within 4Å: Chain A: I.659, I.663, F.666, V.667 Chain B: F.590, L.591, Y.594, F.633, T.636, L.670 Ligands: POV.11 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.590, B:L.591, B:F.633, B:T.636, B:L.670, A:I.659, A:I.663, A:V.667 pi-Stacking: B:Y.594 N8R.16: 11 residues within 4Å: Chain B: I.659, I.663, F.666, V.667 Chain C: F.590, L.591, Y.594, F.633, T.636, L.670 Ligands: POV.18 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:F.590, C:L.591, C:Y.594, C:Y.594, C:F.633, C:T.636, C:L.670, B:I.659, B:I.663, B:V.667 N8R.29: 11 residues within 4Å: Chain C: I.659, I.663, F.666, V.667 Chain D: F.590, L.591, Y.594, F.633, T.636, L.670 Ligands: POV.25 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:I.659, C:I.663, C:V.667, D:F.590, D:L.591, D:Y.594, D:Y.594, D:F.633, D:T.636, D:L.670

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

NA.9: 4 residues within 4Å: Chain A: G.638 Chain B: G.638 Chain C: G.638 Chain D: G.638 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.638 NA.30: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neuberger, A. et al., Structural mechanism of TRPV3 channel inhibition by the anesthetic dyclonine. Nat Commun (2022)

Release Date

2022-06-08

Peptides

Transient receptor potential cation channel subfamily V member 3: 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 3