SMTL ID : 9je5.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.53 Å

Oligo State

homo-tetramer

Ligands

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

POV.1: 13 residues within 4Å: Chain A: L.591, Y.594, I.595, S.626, V.629, L.630, F.633 Chain D: I.644, Q.645, F.656, I.659, I.663, V.667 Ligand excluded by PLIP POV.2: 6 residues within 4Å: Chain A: L.599, V.603, S.624, F.625, S.626 Chain B: Y.460 Ligand excluded by PLIP POV.3: 12 residues within 4Å: Chain A: L.443, S.444, W.493, C.496, I.497, V.499, K.500, E.501, H.523, F.526, Y.564, Y.565 Ligand excluded by PLIP POV.4: 8 residues within 4Å: Chain A: W.433, K.438, F.441, F.442, F.445, Y.565, F.569, Q.570 Ligand excluded by PLIP POV.6: 7 residues within 4Å: Chain A: S.571 Chain D: I.516, K.581, L.584, H.585, L.588, F.592 Ligand excluded by PLIP POV.7: 7 residues within 4Å: Chain A: I.516, K.581, L.584, H.585, L.588, F.592 Chain B: S.571 Ligand excluded by PLIP POV.8: 13 residues within 4Å: Chain A: I.644, Q.645, F.656, I.659, I.663, V.667 Chain B: L.591, Y.594, I.595, S.626, V.629, L.630, F.633 Ligand excluded by PLIP POV.9: 6 residues within 4Å: Chain B: L.599, V.603, S.624, F.625, S.626 Chain C: Y.460 Ligand excluded by PLIP POV.10: 12 residues within 4Å: Chain B: L.443, S.444, W.493, C.496, I.497, V.499, K.500, E.501, H.523, F.526, Y.564, Y.565 Ligand excluded by PLIP POV.11: 8 residues within 4Å: Chain B: W.433, K.438, F.441, F.442, F.445, Y.565, F.569, Q.570 Ligand excluded by PLIP POV.13: 7 residues within 4Å: Chain B: I.516, K.581, L.584, H.585, L.588, F.592 Chain C: S.571 Ligand excluded by PLIP POV.14: 13 residues within 4Å: Chain B: I.644, Q.645, F.656, I.659, I.663, V.667 Chain C: L.591, Y.594, I.595, S.626, V.629, L.630, F.633 Ligand excluded by PLIP POV.15: 6 residues within 4Å: Chain C: L.599, V.603, S.624, F.625, S.626 Chain D: Y.460 Ligand excluded by PLIP POV.16: 12 residues within 4Å: Chain C: L.443, S.444, W.493, C.496, I.497, V.499, K.500, E.501, H.523, F.526, Y.564, Y.565 Ligand excluded by PLIP POV.17: 8 residues within 4Å: Chain C: W.433, K.438, F.441, F.442, F.445, Y.565, F.569, Q.570 Ligand excluded by PLIP POV.19: 7 residues within 4Å: Chain C: I.516, K.581, L.584, H.585, L.588, F.592 Chain D: S.571 Ligand excluded by PLIP POV.20: 13 residues within 4Å: Chain C: I.644, Q.645, F.656, I.659, I.663, V.667 Chain D: L.591, Y.594, I.595, S.626, V.629, L.630, F.633 Ligand excluded by PLIP POV.21: 6 residues within 4Å: Chain A: Y.460 Chain D: L.599, V.603, S.624, F.625, S.626 Ligand excluded by PLIP POV.22: 12 residues within 4Å: Chain D: L.443, S.444, W.493, C.496, I.497, V.499, K.500, E.501, H.523, F.526, Y.564, Y.565 Ligand excluded by PLIP POV.23: 8 residues within 4Å: Chain D: W.433, K.438, F.441, F.442, F.445, Y.565, F.569, Q.570 Ligand excluded by PLIP

4 x 01: (3~{S})-3,7-dimethyloct-6-enal

01.5: 3 residues within 4Å: Chain A: W.521, F.522, I.579 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.521, A:W.521, A:F.522, A:I.579 01.12: 3 residues within 4Å: Chain B: W.521, F.522, I.579 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.521, B:W.521, B:F.522, B:I.579 01.18: 3 residues within 4Å: Chain C: W.521, F.522, I.579 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.521, C:W.521, C:F.522, C:I.579 01.24: 3 residues within 4Å: Chain D: W.521, F.522, I.579 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:W.521, D:W.521, D:F.522, D:I.579

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.
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Transient receptor potential cation channel subfamily V member 3

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