SMTL ID : 9jeg.1

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

POV.1: 16 residues within 4Å: Chain A: L.591, Y.594, I.595, L.598, S.626, D.627, L.630, F.633, T.636 Chain D: I.644, P.651, I.652, F.656, I.659, I.663, V.667 Ligand excluded by PLIP POV.2: 12 residues within 4Å: Chain A: L.443, S.444, K.500, E.501, F.522, H.523, F.526, Y.564, Y.565, E.702, F.703, M.706 Ligand excluded by PLIP POV.3: 11 residues within 4Å: Chain A: W.433, H.439, F.441, F.442, L.443, F.445, Y.565, G.568, F.569, Q.570, R.696 Ligand excluded by PLIP POV.6: 7 residues within 4Å: Chain A: S.571, M.572 Chain D: Q.514, L.584, H.585, L.588, F.592 Ligand excluded by PLIP POV.7: 7 residues within 4Å: Chain A: Q.514, L.584, H.585, L.588, F.592 Chain B: S.571, M.572 Ligand excluded by PLIP POV.8: 16 residues within 4Å: Chain A: I.644, P.651, I.652, F.656, I.659, I.663, V.667 Chain B: L.591, Y.594, I.595, L.598, S.626, D.627, L.630, F.633, T.636 Ligand excluded by PLIP POV.9: 12 residues within 4Å: Chain B: L.443, S.444, K.500, E.501, F.522, H.523, F.526, Y.564, Y.565, E.702, F.703, M.706 Ligand excluded by PLIP POV.10: 11 residues within 4Å: Chain B: W.433, H.439, F.441, F.442, L.443, F.445, Y.565, G.568, F.569, Q.570, R.696 Ligand excluded by PLIP POV.13: 7 residues within 4Å: Chain B: Q.514, L.584, H.585, L.588, F.592 Chain C: S.571, M.572 Ligand excluded by PLIP POV.14: 16 residues within 4Å: Chain B: I.644, P.651, I.652, F.656, I.659, I.663, V.667 Chain C: L.591, Y.594, I.595, L.598, S.626, D.627, L.630, F.633, T.636 Ligand excluded by PLIP POV.15: 12 residues within 4Å: Chain C: L.443, S.444, K.500, E.501, F.522, H.523, F.526, Y.564, Y.565, E.702, F.703, M.706 Ligand excluded by PLIP POV.16: 11 residues within 4Å: Chain C: W.433, H.439, F.441, F.442, L.443, F.445, Y.565, G.568, F.569, Q.570, R.696 Ligand excluded by PLIP POV.20: 7 residues within 4Å: Chain C: Q.514, L.584, H.585, L.588, F.592 Chain D: S.571, M.572 Ligand excluded by PLIP POV.21: 16 residues within 4Å: Chain C: I.644, P.651, I.652, F.656, I.659, I.663, V.667 Chain D: L.591, Y.594, I.595, L.598, S.626, D.627, L.630, F.633, T.636 Ligand excluded by PLIP POV.22: 12 residues within 4Å: Chain D: L.443, S.444, K.500, E.501, F.522, H.523, F.526, Y.564, Y.565, E.702, F.703, M.706 Ligand excluded by PLIP POV.23: 11 residues within 4Å: Chain D: W.433, H.439, F.441, F.442, L.443, F.445, Y.565, G.568, F.569, Q.570, R.696 Ligand excluded by PLIP

8 x 01: (~{Z})-5-methyl-2-propan-2-yl-hex-2-enal

01.4: 7 residues within 4Å: Chain A: W.521, F.522, Q.580, I.583 Chain D: F.597, L.664 Ligands: 01.19 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:W.521, A:W.521, A:W.521, A:F.522, A:I.583, A:I.583, D:F.597, D:L.664 01.5: 11 residues within 4Å: Chain A: F.601, F.656, L.657, T.660, L.664 Chain B: W.521, L.553, A.556, L.557, A.560 Ligands: 01.11 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.656, A:L.657, A:T.660, A:L.664, B:W.521, B:L.553, B:A.556 01.11: 7 residues within 4Å: Chain A: F.597, L.664 Chain B: W.521, F.522, Q.580, I.583 Ligands: 01.5 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:F.597, A:L.664, B:W.521, B:W.521, B:W.521, B:F.522, B:I.583, B:I.583 01.12: 11 residues within 4Å: Chain B: F.601, F.656, L.657, T.660, L.664 Chain C: W.521, L.553, A.556, L.557, A.560 Ligands: 01.17 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:W.521, C:L.553, C:A.556, B:F.656, B:L.657, B:T.660, B:L.664 01.17: 7 residues within 4Å: Chain B: F.597, L.664 Chain C: W.521, F.522, Q.580, I.583 Ligands: 01.12 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:W.521, C:W.521, C:W.521, C:F.522, C:I.583, C:I.583, B:F.597, B:L.664 01.18: 11 residues within 4Å: Chain C: F.601, F.656, L.657, T.660, L.664 Chain D: W.521, L.553, A.556, L.557, A.560 Ligands: 01.24 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:F.656, C:L.657, C:T.660, C:L.664, D:W.521, D:L.553, D:A.556 01.19: 11 residues within 4Å: Chain A: W.521, L.553, A.556, L.557, A.560 Chain D: F.601, F.656, L.657, T.660, L.664 Ligands: 01.4 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:F.656, D:L.657, D:T.660, D:L.664, A:W.521, A:L.553, A:A.556 01.24: 7 residues within 4Å: Chain C: F.597, L.664 Chain D: W.521, F.522, Q.580, I.583 Ligands: 01.18 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:W.521, D:W.521, D:W.521, D:F.522, D:I.583, D:I.583, C:F.597, C:L.664

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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