SMTL ID : 8v6l.1

Open-state cryo-EM structure of human TRPV3 in presence of tetrahydrocannabivarin (THCV) in cNW30 nanodiscs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

POV.1: 2 residues within 4Å: Chain A: Q.514, I.516 Ligand excluded by PLIP POV.2: 14 residues within 4Å: Chain A: K.435, H.439, M.440, L.443, S.444, F.447, W.493, K.500, E.501, F.526, Y.565, F.703, M.706, L.707 Ligand excluded by PLIP POV.3: 9 residues within 4Å: Chain A: S.624, F.625, S.626 Chain D: I.453, T.456, L.457, Y.460, Y.461 Ligands: POV.9 Ligand excluded by PLIP POV.5: 11 residues within 4Å: Chain A: H.430, W.433, K.434, K.438, M.562, G.568, F.569, Q.570, S.571, M.572 Chain B: F.592 Ligand excluded by PLIP POV.6: 15 residues within 4Å: Chain A: I.652, L.655, F.656, I.663, V.667 Chain D: F.590, Y.594, L.598, S.626, V.629, F.633, I.637, L.670 Ligands: POV.26, I8E.27 Ligand excluded by PLIP POV.9: 15 residues within 4Å: Chain A: F.590, Y.594, L.598, S.626, V.629, F.633, I.637, L.670 Chain B: I.652, L.655, F.656, I.663, V.667 Ligands: POV.3, I8E.4 Ligand excluded by PLIP POV.10: 2 residues within 4Å: Chain B: Q.514, I.516 Ligand excluded by PLIP POV.11: 15 residues within 4Å: Chain B: F.590, Y.594, L.598, S.626, V.629, F.633, I.637, L.670 Chain C: I.652, L.655, F.656, I.663, V.667 Ligands: POV.13, I8E.14 Ligand excluded by PLIP POV.12: 14 residues within 4Å: Chain B: K.435, H.439, M.440, L.443, S.444, F.447, W.493, K.500, E.501, F.526, Y.565, F.703, M.706, L.707 Ligand excluded by PLIP POV.13: 9 residues within 4Å: Chain A: I.453, T.456, Y.460, Y.461 Chain B: V.603, S.624, F.625, S.626 Ligands: POV.11 Ligand excluded by PLIP POV.15: 11 residues within 4Å: Chain B: H.430, W.433, K.434, K.438, M.562, G.568, F.569, Q.570, S.571, M.572 Chain C: F.592 Ligand excluded by PLIP POV.17: 2 residues within 4Å: Chain C: Q.514, I.516 Ligand excluded by PLIP POV.18: 15 residues within 4Å: Chain C: F.590, Y.594, L.598, S.626, V.629, F.633, I.637, L.670 Chain D: I.652, L.655, F.656, I.663, V.667 Ligands: POV.20, I8E.21 Ligand excluded by PLIP POV.19: 14 residues within 4Å: Chain C: K.435, H.439, M.440, L.443, S.444, F.447, W.493, K.500, E.501, F.526, Y.565, F.703, M.706, L.707 Ligand excluded by PLIP POV.20: 9 residues within 4Å: Chain B: I.453, T.456, Y.460, Y.461 Chain C: V.603, S.624, F.625, S.626 Ligands: POV.18 Ligand excluded by PLIP POV.22: 11 residues within 4Å: Chain C: H.430, W.433, K.434, K.438, M.562, G.568, F.569, Q.570, S.571, M.572 Chain D: F.592 Ligand excluded by PLIP POV.23: 11 residues within 4Å: Chain A: F.592 Chain D: H.430, W.433, K.434, K.438, M.562, G.568, F.569, Q.570, S.571, M.572 Ligand excluded by PLIP POV.24: 2 residues within 4Å: Chain D: Q.514, I.516 Ligand excluded by PLIP POV.25: 14 residues within 4Å: Chain D: K.435, H.439, M.440, L.443, S.444, F.447, W.493, K.500, E.501, F.526, Y.565, F.703, M.706, L.707 Ligand excluded by PLIP POV.26: 9 residues within 4Å: Chain C: I.453, T.456, Y.460, Y.461 Chain D: V.603, S.624, F.625, S.626 Ligands: POV.6 Ligand excluded by PLIP

4 x I8E: Tetrahydrocannabivarin(Non-covalent)

I8E.4: 11 residues within 4Å: Chain A: W.521, F.522, L.557, A.560, N.561, L.563, I.579, I.583 Chain B: F.597, F.601 Ligands: POV.9 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.521, A:F.522, A:L.557, A:L.563, A:I.579, A:I.583, B:F.597, B:F.601 Hydrogen bonds: A:N.561 I8E.14: 11 residues within 4Å: Chain B: W.521, F.522, L.557, A.560, N.561, L.563, I.579, I.583 Chain C: F.597, F.601 Ligands: POV.11 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:W.521, B:F.522, B:L.557, B:L.563, B:I.579, B:I.583, C:F.597, C:F.601 Hydrogen bonds: B:N.561 I8E.21: 11 residues within 4Å: Chain C: W.521, F.522, L.557, A.560, N.561, L.563, I.579, I.583 Chain D: F.597, F.601 Ligands: POV.18 9 PLIP interactions: 2 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:F.597, D:F.601, C:W.521, C:F.522, C:L.557, C:L.563, C:I.579, C:I.583 Hydrogen bonds: C:N.561 I8E.27: 11 residues within 4Å: Chain A: F.597, F.601 Chain D: W.521, F.522, L.557, A.560, N.561, L.563, I.579, I.583 Ligands: POV.6 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain D Hydrophobic interactions: A:F.597, A:F.601, D:W.521, D:F.522, D:L.557, D:L.563, D:I.579, D:I.583 Hydrogen bonds: D:N.561

3 x NA: SODIUM ION(Non-functional Binders)

NA.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nadezhdin, K.D. et al., TRPV3 activation by different agonists accompanied by lipid dissociation from the vanilloid site. Sci Adv (2024)

Release Date

2024-04-17

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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