SMTL ID : 8v6m.1

Inactivated-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

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

POV.1: 28 residues within 4Å: Chain A: I.583, L.588, F.590, L.591, Y.594, I.595, L.598, S.626, V.629, L.630, F.633, T.636, I.637, L.669 Chain B: I.644, Q.645, P.651, I.652, L.655, F.656, I.659, T.660, V.662, I.663, L.664, F.666 Ligands: I8E.3, POV.16 18 PLIP interactions: 10 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:L.591, A:Y.594, A:Y.594, A:I.595, A:L.598, A:V.629, A:L.630, A:F.633, A:T.636, B:I.652, B:L.655, B:I.659, B:I.659, B:I.663, B:I.663, B:F.666, B:F.666 Hydrogen bonds: A:S.626 POV.2: 24 residues within 4Å: Chain A: K.435, F.436, H.439, M.440, F.441, L.443, S.444, F.447, W.493, C.496, I.497, K.500, E.501, F.526, Y.564, Y.565, T.699, E.702, F.703, M.706, L.707, P.708, L.711, F.715 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:H.439, A:F.447, A:K.500, A:M.706 Salt bridges: A:K.500, A:E.702 POV.4: 22 residues within 4Å: Chain A: F.445, F.449, I.453, T.456, L.457, Y.460, Y.461, R.464, W.559, M.562, Y.565, T.566 Chain B: F.592, I.595, V.596, L.599, V.603, S.624, F.625, S.626, V.629 Ligands: POV.8 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:T.456, A:W.559, A:W.559, B:F.592, B:F.592, B:I.595, B:V.596, B:L.599 Hydrogen bonds: A:Y.460, B:F.625 POV.8: 28 residues within 4Å: Chain B: I.583, L.588, F.590, L.591, Y.594, I.595, L.598, S.626, V.629, L.630, F.633, T.636, I.637, L.669 Chain C: I.644, Q.645, P.651, I.652, L.655, F.656, I.659, T.660, V.662, I.663, L.664, F.666 Ligands: POV.4, I8E.10 18 PLIP interactions: 8 interactions with chain C, 10 interactions with chain B Hydrophobic interactions: C:I.652, C:L.655, C:I.659, C:I.659, C:I.663, C:I.663, C:F.666, C:F.666, B:L.591, B:Y.594, B:Y.594, B:I.595, B:L.598, B:V.629, B:L.630, B:F.633, B:T.636 Hydrogen bonds: B:S.626 POV.9: 24 residues within 4Å: Chain B: K.435, F.436, H.439, M.440, F.441, L.443, S.444, F.447, W.493, C.496, I.497, K.500, E.501, F.526, Y.564, Y.565, T.699, E.702, F.703, M.706, L.707, P.708, L.711, F.715 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:H.439, B:F.447, B:K.500, B:M.706 Salt bridges: B:K.500, B:E.702 POV.11: 21 residues within 4Å: Chain B: F.445, F.449, I.453, T.456, L.457, Y.460, Y.461, W.559, M.562, Y.565, T.566 Chain C: F.592, I.595, V.596, L.599, V.603, S.624, F.625, S.626, V.629 Ligands: POV.12 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:F.592, C:F.592, C:I.595, C:V.596, C:L.599, B:T.456, B:W.559, B:W.559 Hydrogen bonds: C:F.625, B:Y.460 POV.12: 28 residues within 4Å: Chain C: I.583, L.588, F.590, L.591, Y.594, I.595, L.598, S.626, V.629, L.630, F.633, T.636, I.637, L.669 Chain D: I.644, Q.645, P.651, I.652, L.655, F.656, I.659, T.660, V.662, I.663, L.664, F.666 Ligands: POV.11, I8E.14 18 PLIP interactions: 10 interactions with chain C, 8 interactions with chain D Hydrophobic interactions: C:L.591, C:Y.594, C:Y.594, C:I.595, C:L.598, C:V.629, C:L.630, C:F.633, C:T.636, D:I.652, D:L.655, D:I.659, D:I.659, D:I.663, D:I.663, D:F.666, D:F.666 Hydrogen bonds: C:S.626 POV.13: 24 residues within 4Å: Chain C: K.435, F.436, H.439, M.440, F.441, L.443, S.444, F.447, W.493, C.496, I.497, K.500, E.501, F.526, Y.564, Y.565, T.699, E.702, F.703, M.706, L.707, P.708, L.711, F.715 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:H.439, C:F.447, C:K.500, C:M.706 Salt bridges: C:K.500, C:E.702 POV.15: 21 residues within 4Å: Chain C: F.445, F.449, I.453, T.456, L.457, Y.460, Y.461, W.559, M.562, Y.565, T.566 Chain D: F.592, I.595, V.596, L.599, V.603, S.624, F.625, S.626, V.629 Ligands: POV.17 10 PLIP interactions: 6 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:F.592, D:F.592, D:I.595, D:V.596, D:L.599, C:T.456, C:W.559, C:W.559 Hydrogen bonds: D:F.625, C:Y.460 POV.16: 21 residues within 4Å: Chain A: F.592, I.595, V.596, L.599, V.603, S.624, F.625, S.626, V.629 Chain D: F.445, F.449, I.453, T.456, L.457, Y.460, Y.461, W.559, M.562, Y.565, T.566 Ligands: POV.1 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:F.592, A:F.592, A:I.595, A:V.596, A:L.599, D:T.456, D:W.559, D:W.559 Hydrogen bonds: A:F.625, D:Y.460 POV.17: 28 residues within 4Å: Chain A: I.644, Q.645, P.651, I.652, L.655, F.656, I.659, T.660, V.662, I.663, L.664, F.666 Chain D: I.583, L.588, F.590, L.591, Y.594, I.595, L.598, S.626, V.629, L.630, F.633, T.636, I.637, L.669 Ligands: POV.15, I8E.19 18 PLIP interactions: 10 interactions with chain D, 8 interactions with chain A Hydrophobic interactions: D:L.591, D:Y.594, D:Y.594, D:I.595, D:L.598, D:V.629, D:L.630, D:F.633, D:T.636, A:I.652, A:L.655, A:I.659, A:I.659, A:I.663, A:I.663, A:F.666, A:F.666 Hydrogen bonds: D:S.626 POV.18: 24 residues within 4Å: Chain D: K.435, F.436, H.439, M.440, F.441, L.443, S.444, F.447, W.493, C.496, I.497, K.500, E.501, F.526, Y.564, Y.565, T.699, E.702, F.703, M.706, L.707, P.708, L.711, F.715 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:H.439, D:F.447, D:K.500, D:M.706 Salt bridges: D:K.500, D:E.702

4 x I8E: Tetrahydrocannabivarin(Non-covalent)

I8E.3: 17 residues within 4Å: Chain A: W.521, F.522, V.525, A.556, L.557, A.560, N.561, L.563, I.579, I.583 Chain B: F.597, F.601, F.656, L.657, T.660, L.664 Ligands: POV.1 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:F.597, B:F.601, B:T.660, A:W.521, A:F.522, A:A.556, A:L.557, A:L.563, A:I.579 Hydrogen bonds: A:N.561 I8E.10: 17 residues within 4Å: Chain B: W.521, F.522, V.525, A.556, L.557, A.560, N.561, L.563, I.579, I.583 Chain C: F.597, F.601, F.656, L.657, T.660, L.664 Ligands: POV.8 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: C:F.597, C:F.601, C:T.660, B:W.521, B:F.522, B:A.556, B:L.557, B:L.563, B:I.579 Hydrogen bonds: B:N.561 I8E.14: 17 residues within 4Å: Chain C: W.521, F.522, V.525, A.556, L.557, A.560, N.561, L.563, I.579, I.583 Chain D: F.597, F.601, F.656, L.657, T.660, L.664 Ligands: POV.12 10 PLIP interactions: 3 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:F.597, D:F.601, D:T.660, C:W.521, C:F.522, C:A.556, C:L.557, C:L.563, C:I.579 Hydrogen bonds: C:N.561 I8E.19: 17 residues within 4Å: Chain A: F.597, F.601, F.656, L.657, T.660, L.664 Chain D: W.521, F.522, V.525, A.556, L.557, A.560, N.561, L.563, I.579, I.583 Ligands: POV.17 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:W.521, D:F.522, D:A.556, D:L.557, D:L.563, D:I.579, A:F.597, A:F.601, A:T.660 Hydrogen bonds: D:N.561

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

NA.5: 8 residues within 4Å: Chain A: G.638, L.639 Chain B: G.638, L.639 Chain C: G.638, L.639 Chain D: G.638, L.639 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.638 NA.6: 4 residues within 4Å: Chain A: G.638 Chain B: G.638 Chain C: G.638 Chain D: G.638 No protein-ligand interaction detected (PLIP) NA.7: 4 residues within 4Å: Chain A: M.677 Chain B: M.677 Chain C: M.677 Chain D: M.677 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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