SMTL ID : 9jef.1

Cryo-EM structure of human TRPV3 in complex with linalool determined in MSP2N2 nanodisc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.62 Å

Oligo State

homo-tetramer

Ligands

4 x 01: (3~{R})-3,7-dimethylocta-1,6-dien-3-ol

01.1: 7 residues within 4Å: Chain A: L.553, A.556, L.557, A.560 Chain D: F.601, L.657, L.664 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:F.601, D:L.657, D:L.664, A:A.556, A:L.557, A:A.560 01.7: 7 residues within 4Å: Chain A: F.601, L.657, L.664 Chain B: L.553, A.556, L.557, A.560 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.601, A:L.657, A:L.664, B:A.556, B:L.557, B:A.560 01.13: 8 residues within 4Å: Chain B: F.601, L.657, T.660, L.664 Chain C: L.553, A.556, L.557, A.560 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:A.556, C:L.557, C:A.560, B:F.601, B:L.657, B:T.660, B:L.664 01.19: 8 residues within 4Å: Chain C: F.601, L.657, T.660, L.664 Chain D: L.553, A.556, L.557, A.560 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:F.601, C:L.657, C:T.660, C:L.664, D:A.556, D:L.557, D:A.560

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

POV.2: 14 residues within 4Å: Chain A: L.591, Y.594, L.598, S.626, V.629, F.633 Chain D: I.644, I.652, L.655, F.656, I.659, I.663, F.666, V.667 Ligand excluded by PLIP POV.3: 9 residues within 4Å: Chain A: L.532, E.546, A.549, C.550, L.553 Chain D: Y.650, P.651, I.652, F.656 Ligand excluded by PLIP POV.4: 14 residues within 4Å: Chain A: K.438, H.439, F.441, F.442, F.445, F.449, M.562, Y.565, G.568, F.569, Q.570, R.696 Chain D: F.592, V.596 Ligand excluded by PLIP POV.5: 18 residues within 4Å: Chain A: H.439, M.440, L.443, S.444, W.493, M.495, C.496, I.497, V.499, K.500, E.501, F.526, Y.564, Y.565, E.702, M.706, L.707, L.711 Ligand excluded by PLIP POV.6: 7 residues within 4Å: Chain A: L.584, H.585, L.588, F.592, I.595 Chain B: S.571, M.572 Ligand excluded by PLIP POV.8: 13 residues within 4Å: Chain A: I.644, L.655, F.656, I.659, I.663, F.666, V.667 Chain B: L.591, Y.594, L.598, S.626, V.629, F.633 Ligand excluded by PLIP POV.9: 9 residues within 4Å: Chain A: Y.650, P.651, I.652, F.656 Chain B: L.532, E.546, A.549, C.550, L.553 Ligand excluded by PLIP POV.10: 14 residues within 4Å: Chain A: F.592, V.596 Chain B: K.438, H.439, F.441, F.442, F.445, F.449, M.562, Y.565, G.568, F.569, Q.570, R.696 Ligand excluded by PLIP POV.11: 18 residues within 4Å: Chain B: H.439, M.440, L.443, S.444, W.493, M.495, C.496, I.497, V.499, K.500, E.501, F.526, Y.564, Y.565, E.702, M.706, L.707, L.711 Ligand excluded by PLIP POV.12: 7 residues within 4Å: Chain B: L.584, H.585, L.588, F.592, I.595 Chain C: S.571, M.572 Ligand excluded by PLIP POV.14: 13 residues within 4Å: Chain B: I.652, L.655, F.656, I.659, I.663, F.666, V.667 Chain C: L.591, Y.594, L.598, S.626, V.629, F.633 Ligand excluded by PLIP POV.15: 9 residues within 4Å: Chain B: Y.650, P.651, I.652, F.656 Chain C: L.532, E.546, A.549, C.550, L.553 Ligand excluded by PLIP POV.16: 14 residues within 4Å: Chain B: F.592, V.596 Chain C: K.438, H.439, F.441, F.442, F.445, F.449, M.562, Y.565, G.568, F.569, Q.570, R.696 Ligand excluded by PLIP POV.17: 18 residues within 4Å: Chain C: H.439, M.440, L.443, S.444, W.493, M.495, C.496, I.497, V.499, K.500, E.501, F.526, Y.564, Y.565, E.702, M.706, L.707, L.711 Ligand excluded by PLIP POV.18: 7 residues within 4Å: Chain C: L.584, H.585, L.588, F.592, I.595 Chain D: S.571, M.572 Ligand excluded by PLIP POV.20: 13 residues within 4Å: Chain C: I.644, L.655, F.656, I.659, I.663, F.666, V.667 Chain D: L.591, Y.594, L.598, S.626, V.629, F.633 Ligand excluded by PLIP POV.21: 9 residues within 4Å: Chain C: Y.650, P.651, I.652, F.656 Chain D: L.532, E.546, A.549, C.550, L.553 Ligand excluded by PLIP POV.22: 14 residues within 4Å: Chain C: F.592, V.596 Chain D: K.438, H.439, F.441, F.442, F.445, F.449, M.562, Y.565, G.568, F.569, Q.570, R.696 Ligand excluded by PLIP POV.23: 18 residues within 4Å: Chain D: H.439, M.440, L.443, S.444, W.493, M.495, C.496, I.497, V.499, K.500, E.501, F.526, Y.564, Y.565, E.702, M.706, L.707, L.711 Ligand excluded by PLIP POV.24: 7 residues within 4Å: Chain A: S.571, M.572 Chain D: L.584, H.585, L.588, F.592, I.595 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Plant essential oil targets TRPV3 for skin renewal and structural mechanism of action. Nat Commun (2025)

Release Date

2025-03-26

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.
Show / Hide

Transient receptor potential cation channel subfamily V member 3

Related Entries With Identical Sequence