SMTL ID : 9jee.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.51 Å

Oligo State

homo-tetramer

Ligands

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

POV.1: 10 residues within 4Å: Chain A: S.444, C.496, K.500, E.501, H.523, Y.564, Y.565, F.703, M.706, P.708 Ligand excluded by PLIP POV.2: 10 residues within 4Å: Chain A: Q.514, S.515, I.516, L.584, H.585, L.588, K.589, F.592 Chain B: S.571, M.572 Ligand excluded by PLIP POV.3: 14 residues within 4Å: Chain A: W.433, K.438, H.439, F.441, F.442, L.443, F.445, Y.565, T.566, G.568, F.569, Q.570, S.571 Chain D: F.592 Ligand excluded by PLIP POV.5: 14 residues within 4Å: Chain A: I.644, L.655, F.656, I.659, I.663, F.666 Chain B: F.590, L.591, Y.594, S.626, V.629, L.630, F.633, I.637 Ligand excluded by PLIP POV.6: 6 residues within 4Å: Chain A: T.456, Y.460, Y.461 Chain D: S.624, F.625, S.626 Ligand excluded by PLIP POV.7: 6 residues within 4Å: Chain A: S.624, F.625, S.626 Chain B: T.456, Y.460, Y.461 Ligand excluded by PLIP POV.8: 10 residues within 4Å: Chain B: S.444, C.496, K.500, E.501, H.523, Y.564, Y.565, F.703, M.706, P.708 Ligand excluded by PLIP POV.9: 10 residues within 4Å: Chain B: Q.514, S.515, I.516, L.584, H.585, L.588, K.589, F.592 Chain C: S.571, M.572 Ligand excluded by PLIP POV.10: 14 residues within 4Å: Chain A: F.592 Chain B: W.433, K.438, H.439, F.441, F.442, L.443, F.445, Y.565, T.566, G.568, F.569, Q.570, S.571 Ligand excluded by PLIP POV.12: 14 residues within 4Å: Chain B: I.644, L.655, F.656, I.659, I.663, F.666 Chain C: F.590, L.591, Y.594, S.626, V.629, L.630, F.633, I.637 Ligand excluded by PLIP POV.13: 6 residues within 4Å: Chain B: S.624, F.625, S.626 Chain C: T.456, Y.460, Y.461 Ligand excluded by PLIP POV.14: 10 residues within 4Å: Chain C: S.444, C.496, K.500, E.501, H.523, Y.564, Y.565, F.703, M.706, P.708 Ligand excluded by PLIP POV.15: 10 residues within 4Å: Chain C: Q.514, S.515, I.516, L.584, H.585, L.588, K.589, F.592 Chain D: S.571, M.572 Ligand excluded by PLIP POV.16: 14 residues within 4Å: Chain B: F.592 Chain C: W.433, K.438, H.439, F.441, F.442, L.443, F.445, Y.565, T.566, G.568, F.569, Q.570, S.571 Ligand excluded by PLIP POV.18: 14 residues within 4Å: Chain C: I.644, L.655, F.656, I.659, I.663, F.666 Chain D: F.590, L.591, Y.594, S.626, V.629, L.630, F.633, I.637 Ligand excluded by PLIP POV.19: 14 residues within 4Å: Chain A: F.590, L.591, Y.594, S.626, V.629, L.630, F.633, I.637 Chain D: I.644, L.655, F.656, I.659, I.663, F.666 Ligand excluded by PLIP POV.20: 6 residues within 4Å: Chain C: S.624, F.625, S.626 Chain D: T.456, Y.460, Y.461 Ligand excluded by PLIP POV.21: 10 residues within 4Å: Chain D: S.444, C.496, K.500, E.501, H.523, Y.564, Y.565, F.703, M.706, P.708 Ligand excluded by PLIP POV.22: 10 residues within 4Å: Chain A: S.571, M.572 Chain D: Q.514, S.515, I.516, L.584, H.585, L.588, K.589, F.592 Ligand excluded by PLIP POV.23: 14 residues within 4Å: Chain C: F.592 Chain D: W.433, K.438, H.439, F.441, F.442, L.443, F.445, Y.565, T.566, G.568, F.569, Q.570, S.571 Ligand excluded by PLIP

4 x GRQ: Geranaldehyde

GRQ.4: 9 residues within 4Å: Chain A: W.521, F.522, L.557, A.560, L.563, S.576, I.579, Q.580, I.583 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.521, A:F.522, A:F.522, A:L.557, A:A.560, A:Q.580 GRQ.11: 9 residues within 4Å: Chain B: W.521, F.522, L.557, A.560, L.563, S.576, I.579, Q.580, I.583 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.521, B:F.522, B:F.522, B:L.557, B:A.560, B:Q.580 GRQ.17: 9 residues within 4Å: Chain C: W.521, F.522, L.557, A.560, L.563, S.576, I.579, Q.580, I.583 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.521, C:F.522, C:F.522, C:L.557, C:A.560, C:Q.580 GRQ.24: 9 residues within 4Å: Chain D: W.521, F.522, L.557, A.560, L.563, S.576, I.579, Q.580, I.583 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:W.521, D:F.522, D:F.522, D:L.557, D:A.560, D:Q.580

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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