SMTL ID : 8v6n.1

Open-state cryo-EM structure of human TRPV3 in presence of 2-APB 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: 23 residues within 4Å: Chain A: F.590, L.591, Y.594, S.624, S.626, D.627, V.629, L.630, F.633, T.636, I.637, L.670, L.673 Chain B: I.644, I.652, L.655, F.656, I.659, T.660, I.663, V.667 Ligands: POV.4, POV.11 Ligand excluded by PLIP POV.3: 15 residues within 4Å: Chain A: W.433, K.434, K.435, F.436, K.438, H.439, F.441, F.442, F.445, Y.565, T.566, F.569, L.711, F.715 Ligands: POV.15 Ligand excluded by PLIP POV.4: 16 residues within 4Å: Chain A: L.588, L.591, F.592, V.596, L.599, S.624, F.625, S.626 Chain D: F.449, T.456, Y.460, W.559, M.562 Ligands: POV.1, POV.27, POV.30 Ligand excluded by PLIP POV.7: 9 residues within 4Å: Chain A: F.445, C.446, F.449, F.450, I.453, L.457, Y.461, L.482 Ligands: POV.15 Ligand excluded by PLIP POV.8: 23 residues within 4Å: Chain A: I.644, I.652, L.655, F.656, I.659, T.660, I.663, V.667 Chain D: F.590, L.591, Y.594, S.624, S.626, D.627, V.629, L.630, F.633, T.636, I.637, L.670, L.673 Ligands: POV.9, POV.31 Ligand excluded by PLIP POV.9: 16 residues within 4Å: Chain A: F.601, Y.650, P.651, I.652, L.653, F.656, T.660 Chain D: I.528, L.532, E.546, A.549, L.553, A.556, L.557 Ligands: POV.8, ACD.29 Ligand excluded by PLIP POV.11: 16 residues within 4Å: Chain A: I.528, L.532, E.546, A.549, L.553, A.556, L.557 Chain B: F.601, Y.650, P.651, I.652, L.653, F.656, T.660 Ligands: POV.1, ACD.2 Ligand excluded by PLIP POV.12: 23 residues within 4Å: Chain B: F.590, L.591, Y.594, S.624, S.626, D.627, V.629, L.630, F.633, T.636, I.637, L.670, L.673 Chain C: I.644, I.652, L.655, F.656, I.659, T.660, I.663, V.667 Ligands: POV.15, POV.19 Ligand excluded by PLIP POV.14: 16 residues within 4Å: Chain B: W.433, K.434, K.435, F.436, K.438, H.439, F.441, F.442, F.445, M.562, Y.565, T.566, F.569, L.711, F.715 Ligands: POV.23 Ligand excluded by PLIP POV.15: 15 residues within 4Å: Chain A: F.449, T.456, Y.460, W.559 Chain B: L.588, L.591, F.592, V.596, L.599, S.624, F.625, S.626 Ligands: POV.3, POV.7, POV.12 Ligand excluded by PLIP POV.18: 8 residues within 4Å: Chain B: C.446, F.449, F.450, I.453, L.457, Y.461, L.482 Ligands: POV.23 Ligand excluded by PLIP POV.19: 16 residues within 4Å: Chain B: I.528, L.532, E.546, A.549, L.553, A.556, L.557 Chain C: F.601, Y.650, P.651, I.652, L.653, F.656, T.660 Ligands: POV.12, ACD.13 Ligand excluded by PLIP POV.20: 23 residues within 4Å: Chain C: F.590, L.591, Y.594, S.624, S.626, D.627, V.629, L.630, F.633, T.636, I.637, L.670, L.673 Chain D: I.644, I.652, L.655, F.656, I.659, T.660, I.663, V.667 Ligands: POV.23, POV.28 Ligand excluded by PLIP POV.22: 16 residues within 4Å: Chain C: W.433, K.434, K.435, F.436, K.438, H.439, F.441, F.442, F.445, M.562, Y.565, T.566, F.569, L.711, F.715 Ligands: POV.31 Ligand excluded by PLIP POV.23: 14 residues within 4Å: Chain B: F.449, T.456, Y.460 Chain C: L.588, L.591, F.592, V.596, L.599, S.624, F.625, S.626 Ligands: POV.14, POV.18, POV.20 Ligand excluded by PLIP POV.26: 8 residues within 4Å: Chain C: C.446, F.449, F.450, I.453, L.457, Y.461, L.482 Ligands: POV.31 Ligand excluded by PLIP POV.27: 8 residues within 4Å: Chain D: C.446, F.449, F.450, I.453, L.457, Y.461, L.482 Ligands: POV.4 Ligand excluded by PLIP POV.28: 16 residues within 4Å: Chain C: I.528, L.532, E.546, A.549, L.553, A.556, L.557 Chain D: F.601, Y.650, P.651, I.652, L.653, F.656, T.660 Ligands: POV.20, ACD.21 Ligand excluded by PLIP POV.30: 16 residues within 4Å: Chain D: W.433, K.434, K.435, F.436, K.438, H.439, F.441, F.442, F.445, M.562, Y.565, T.566, F.569, L.711, F.715 Ligands: POV.4 Ligand excluded by PLIP POV.31: 14 residues within 4Å: Chain C: F.449, T.456, Y.460 Chain D: L.588, L.591, F.592, V.596, L.599, S.624, F.625, S.626 Ligands: POV.8, POV.22, POV.26 Ligand excluded by PLIP

4 x ACD: ARACHIDONIC ACID(Non-covalent)

ACD.2: 10 residues within 4Å: Chain A: V.525, I.528, L.557, A.560, L.563, S.576, I.579, Q.580 Chain B: F.597 Ligands: POV.11 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.525, A:I.528, A:L.557, A:L.563, A:I.579, B:F.597 Hydrogen bonds: A:Q.580 ACD.13: 9 residues within 4Å: Chain B: I.528, L.557, A.560, L.563, S.576, I.579, Q.580 Chain C: F.597 Ligands: POV.19 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.528, B:L.557, B:L.563, B:I.579, C:F.597 Hydrogen bonds: B:Q.580 ACD.21: 10 residues within 4Å: Chain C: V.525, I.528, L.557, A.560, L.563, S.576, I.579, Q.580 Chain D: F.597 Ligands: POV.28 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:F.597, C:V.525, C:I.528, C:L.563, C:I.579 Hydrogen bonds: C:Q.580 ACD.29: 10 residues within 4Å: Chain A: F.597 Chain D: V.525, I.528, L.557, A.560, L.563, S.576, I.579, Q.580 Ligands: POV.9 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:V.525, D:L.557, D:L.563, D:I.579, A:F.597 Hydrogen bonds: D:Q.580

8 x FZ4: 2-aminoethyl diphenylborinate(Non-covalent)

FZ4.5: 8 residues within 4Å: Chain A: H.417, L.420, T.421, H.426, L.429, H.430, R.693, R.696 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.420, A:L.429, A:L.429, A:H.430, A:R.693 FZ4.6: 7 residues within 4Å: Chain A: M.440, S.444, W.493, C.496, K.500, Y.564, M.706 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.493, A:Y.564 Hydrogen bonds: A:C.496 FZ4.16: 8 residues within 4Å: Chain B: H.417, L.420, T.421, H.426, L.429, H.430, R.693, R.696 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.420, B:L.429, B:L.429, B:H.430, B:R.693 FZ4.17: 7 residues within 4Å: Chain B: M.440, S.444, W.493, C.496, K.500, Y.564, M.706 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.493, B:Y.564 Hydrogen bonds: B:C.496 FZ4.24: 8 residues within 4Å: Chain C: H.417, L.420, T.421, H.426, L.429, H.430, R.693, R.696 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.420, C:L.429, C:L.429, C:H.430, C:R.693 FZ4.25: 7 residues within 4Å: Chain C: M.440, S.444, W.493, C.496, K.500, Y.564, M.706 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.493, C:Y.564 Hydrogen bonds: C:C.496 FZ4.32: 8 residues within 4Å: Chain D: H.417, L.420, T.421, H.426, L.429, H.430, R.693, R.696 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.420, D:L.429, D:H.430, D:R.693 FZ4.33: 7 residues within 4Å: Chain D: M.440, S.444, W.493, C.496, K.500, Y.564, M.706 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:W.493, D:Y.564 Hydrogen bonds: D:C.496

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

NA.10: 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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