SMTL ID : 6lgp.1

cryo-EM structure of TRPV3 in lipid nanodisc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

POV.1: 17 residues within 4Å: Chain A: L.400, S.401, D.402, W.404, F.405, L.440, A.443, L.446, R.450, S.459, I.462, Q.463, I.466, Q.578 Chain D: F.484 Ligands: PLC.7, POV.22 Ligand excluded by PLIP POV.4: 9 residues within 4Å: Chain A: S.327, K.383, E.384, F.405, H.406, F.409, Y.447, Y.448, M.589 Ligand excluded by PLIP POV.5: 4 residues within 4Å: Chain A: L.467, L.471, F.475 Chain B: S.454 Ligand excluded by PLIP POV.6: 17 residues within 4Å: Chain A: I.535, L.538, F.539, I.542, T.543, I.546, F.549, V.550 Chain B: Y.477, L.481, S.509, V.512, L.513, F.516, T.519 Ligands: POV.9, PLC.10 Ligand excluded by PLIP POV.9: 17 residues within 4Å: Chain A: F.484 Chain B: L.400, S.401, D.402, W.404, F.405, L.440, A.443, L.446, R.450, S.459, I.462, Q.463, I.466, Q.578 Ligands: POV.6, PLC.8 Ligand excluded by PLIP POV.12: 9 residues within 4Å: Chain B: S.327, K.383, E.384, F.405, H.406, F.409, Y.447, Y.448, M.589 Ligand excluded by PLIP POV.13: 4 residues within 4Å: Chain B: L.467, L.471, F.475 Chain C: S.454 Ligand excluded by PLIP POV.14: 17 residues within 4Å: Chain B: I.535, L.538, F.539, I.542, T.543, I.546, F.549, V.550 Chain C: Y.477, L.481, S.509, V.512, L.513, F.516, T.519 Ligands: POV.16, PLC.17 Ligand excluded by PLIP POV.16: 17 residues within 4Å: Chain B: F.484 Chain C: L.400, S.401, D.402, W.404, F.405, L.440, A.443, L.446, R.450, S.459, I.462, Q.463, I.466, Q.578 Ligands: POV.14, PLC.15 Ligand excluded by PLIP POV.19: 9 residues within 4Å: Chain C: S.327, K.383, E.384, F.405, H.406, F.409, Y.447, Y.448, M.589 Ligand excluded by PLIP POV.20: 4 residues within 4Å: Chain C: L.467, L.471, F.475 Chain D: S.454 Ligand excluded by PLIP POV.21: 17 residues within 4Å: Chain C: I.535, L.538, F.539, I.542, T.543, I.546, F.549, V.550 Chain D: Y.477, L.481, S.509, V.512, L.513, F.516, T.519 Ligands: POV.24, PLC.25 Ligand excluded by PLIP POV.22: 17 residues within 4Å: Chain A: Y.477, L.481, S.509, V.512, L.513, F.516, T.519 Chain D: I.535, L.538, F.539, I.542, T.543, I.546, F.549, V.550 Ligands: POV.1, PLC.2 Ligand excluded by PLIP POV.24: 17 residues within 4Å: Chain C: F.484 Chain D: L.400, S.401, D.402, W.404, F.405, L.440, A.443, L.446, R.450, S.459, I.462, Q.463, I.466, Q.578 Ligands: POV.21, PLC.23 Ligand excluded by PLIP POV.27: 9 residues within 4Å: Chain D: S.327, K.383, E.384, F.405, H.406, F.409, Y.447, Y.448, M.589 Ligand excluded by PLIP POV.28: 4 residues within 4Å: Chain A: S.454 Chain D: L.467, L.471, F.475 Ligand excluded by PLIP

12 x PLC: DIUNDECYL PHOSPHATIDYL CHOLINE(Non-covalent)

PLC.2: 11 residues within 4Å: Chain A: I.478, L.482, V.486, S.507, F.508, S.509, D.510 Chain B: Y.343, Y.344, W.442 Ligands: POV.22 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.478, A:L.482, A:V.486, A:F.508, A:F.508, A:F.508, B:W.442, B:W.442 Hydrogen bonds: A:S.507, A:F.508, B:Y.343 Salt bridges: A:D.510 PLC.3: 11 residues within 4Å: Chain A: W.316, K.321, F.324, F.325, F.328, Y.448, G.451, F.452, Q.453, S.454, R.579 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:K.321, A:F.324, A:F.325, A:F.328, A:F.452, A:F.452, A:F.452, A:F.452, A:Q.453 Hydrogen bonds: A:Q.453 Salt bridges: A:K.321, A:R.579 PLC.7: 7 residues within 4Å: Chain A: E.429, A.432, C.433, L.436 Chain D: I.535, F.539 Ligands: POV.1 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.535 PLC.8: 7 residues within 4Å: Chain A: I.535, F.539 Chain B: E.429, A.432, C.433, L.436 Ligands: POV.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.535 PLC.10: 11 residues within 4Å: Chain B: I.478, L.482, V.486, S.507, F.508, S.509, D.510 Chain C: Y.343, Y.344, W.442 Ligands: POV.6 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:I.478, B:L.482, B:V.486, B:F.508, B:F.508, B:F.508, C:W.442, C:W.442 Hydrogen bonds: B:S.507, B:F.508, C:Y.343 Salt bridges: B:D.510 PLC.11: 11 residues within 4Å: Chain B: W.316, K.321, F.324, F.325, F.328, Y.448, G.451, F.452, Q.453, S.454, R.579 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:K.321, B:F.324, B:F.325, B:F.328, B:F.452, B:F.452, B:F.452, B:F.452, B:Q.453 Hydrogen bonds: B:Q.453 Salt bridges: B:K.321, B:R.579 PLC.15: 7 residues within 4Å: Chain B: I.535, F.539 Chain C: E.429, A.432, C.433, L.436 Ligands: POV.16 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.535 PLC.17: 11 residues within 4Å: Chain C: I.478, L.482, V.486, S.507, F.508, S.509, D.510 Chain D: Y.343, Y.344, W.442 Ligands: POV.14 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:I.478, C:L.482, C:V.486, C:F.508, C:F.508, C:F.508, D:W.442, D:W.442 Hydrogen bonds: C:S.507, C:F.508, D:Y.343 Salt bridges: C:D.510 PLC.18: 11 residues within 4Å: Chain C: W.316, K.321, F.324, F.325, F.328, Y.448, G.451, F.452, Q.453, S.454, R.579 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:K.321, C:F.324, C:F.325, C:F.328, C:F.452, C:F.452, C:F.452, C:F.452, C:Q.453 Hydrogen bonds: C:Q.453 Salt bridges: C:K.321, C:R.579 PLC.23: 7 residues within 4Å: Chain C: I.535, F.539 Chain D: E.429, A.432, C.433, L.436 Ligands: POV.24 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.535 PLC.25: 11 residues within 4Å: Chain A: Y.343, Y.344, W.442 Chain D: I.478, L.482, V.486, S.507, F.508, S.509, D.510 Ligands: POV.21 12 PLIP interactions: 9 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:I.478, D:L.482, D:V.486, D:F.508, D:F.508, D:F.508, A:W.442, A:W.442 Hydrogen bonds: D:S.507, D:F.508, A:Y.343 Salt bridges: D:D.510 PLC.26: 11 residues within 4Å: Chain D: W.316, K.321, F.324, F.325, F.328, Y.448, G.451, F.452, Q.453, S.454, R.579 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:K.321, D:F.324, D:F.325, D:F.328, D:F.452, D:F.452, D:F.452, D:F.452, D:Q.453 Hydrogen bonds: D:Q.453 Salt bridges: D:K.321, D:R.579

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimada, H. et al., The structure of lipid nanodisc-reconstituted TRPV3 reveals the gating mechanism. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-06-24

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