SMTL ID : 8v6o.1

Inactivated-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

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

POV.1: 17 residues within 4Å: Chain A: K.581, I.583, L.584, H.585, D.586, V.587, L.588, K.589, F.592, A.675 Chain D: F.442, F.569, S.571, M.572 Ligands: POV.2, POV.33, POV.34 Ligand excluded by PLIP POV.2: 15 residues within 4Å: Chain A: I.595, L.599, Y.622, V.629, L.630 Chain B: Y.650, P.651, I.652, L.653, F.656, T.660, I.663 Ligands: POV.1, POV.3, POV.5 Ligand excluded by PLIP POV.3: 15 residues within 4Å: Chain A: I.595, L.599, Y.622, G.623, S.624, F.625, S.626 Chain D: I.453, T.456, L.457, Y.460, Y.461 Ligands: POV.2, POV.33, POV.34 Ligand excluded by PLIP POV.4: 11 residues within 4Å: Chain A: K.435, F.436, H.439, M.440, M.706, W.710, L.711, R.714, F.715 Ligands: FZ4.7, POV.8 Ligand excluded by PLIP POV.5: 20 residues within 4Å: Chain A: S.518, D.519, A.520, W.521, F.522, L.553, L.557, A.560, N.561, L.563, Y.564, R.567, Q.580, I.583, L.584, Q.695 Chain B: T.660, L.664 Ligands: POV.2, POV.14 Ligand excluded by PLIP POV.8: 21 residues within 4Å: Chain A: W.433, K.438, H.439, F.441, F.442, F.445, F.449, W.559, M.562, Y.565, T.566, G.568, F.569, Q.570, R.696 Chain B: F.592, I.595, V.596 Ligands: POV.4, POV.15, POV.17 Ligand excluded by PLIP POV.9: 12 residues within 4Å: Chain A: C.446, F.449, F.450, I.453, T.454, L.457, Y.461, L.482, Q.483, G.486 Ligands: POV.15, POV.17 Ligand excluded by PLIP POV.10: 16 residues within 4Å: Chain A: V.596, F.597, G.600, F.601, S.607, L.608, Y.650 Chain D: K.545, Y.547, L.548, A.549, V.552, L.553, A.556, A.560 Ligands: POV.40 Ligand excluded by PLIP POV.11: 14 residues within 4Å: Chain A: Y.650, P.651, I.652, L.653, F.656, T.660, I.663 Chain D: I.595, L.599, Y.622, L.630 Ligands: POV.37, POV.38, POV.40 Ligand excluded by PLIP POV.14: 17 residues within 4Å: Chain A: K.545, Y.547, L.548, A.549, V.552, L.553, A.556, A.560 Chain B: V.596, F.597, G.600, F.601, S.607, L.608, K.649, Y.650 Ligands: POV.5 Ligand excluded by PLIP POV.15: 16 residues within 4Å: Chain A: F.442, F.569, S.571 Chain B: K.581, I.583, L.584, H.585, D.586, V.587, L.588, K.589, F.592, A.675 Ligands: POV.8, POV.9, POV.24 Ligand excluded by PLIP POV.16: 18 residues within 4Å: Chain B: K.545, Y.547, L.548, A.549, V.552, L.553, A.556, A.560 Chain C: V.596, F.597, G.600, F.601, S.607, L.608, K.649, Y.650, L.657 Ligands: POV.19 Ligand excluded by PLIP POV.17: 15 residues within 4Å: Chain A: I.453, T.456, L.457, Y.460, Y.461 Chain B: I.595, L.599, Y.622, G.623, S.624, F.625, S.626 Ligands: POV.8, POV.9, POV.24 Ligand excluded by PLIP POV.18: 10 residues within 4Å: Chain B: K.435, F.436, H.439, M.440, M.706, W.710, R.714, F.715 Ligands: FZ4.21, POV.22 Ligand excluded by PLIP POV.19: 20 residues within 4Å: Chain B: S.518, D.519, A.520, W.521, F.522, L.553, L.557, A.560, N.561, L.563, Y.564, R.567, Q.580, I.583, L.584, Q.695 Chain C: T.660, L.664 Ligands: POV.16, POV.24 Ligand excluded by PLIP POV.22: 21 residues within 4Å: Chain B: W.433, K.438, H.439, F.441, F.442, F.445, F.449, W.559, M.562, Y.565, T.566, G.568, F.569, Q.570, R.696 Chain C: F.592, I.595, V.596 Ligands: POV.18, POV.25, POV.26 Ligand excluded by PLIP POV.23: 11 residues within 4Å: Chain B: F.449, F.450, I.453, T.454, L.457, Y.461, L.482, Q.483, G.486 Ligands: POV.25, POV.26 Ligand excluded by PLIP POV.24: 17 residues within 4Å: Chain B: I.595, L.599, Y.622, V.629, L.630, F.633 Chain C: Y.650, P.651, I.652, L.653, F.656, I.659, T.660, I.663 Ligands: POV.15, POV.17, POV.19 Ligand excluded by PLIP POV.25: 16 residues within 4Å: Chain B: F.442, F.569, S.571 Chain C: K.581, I.583, L.584, H.585, D.586, V.587, L.588, K.589, F.592, A.675 Ligands: POV.22, POV.23, POV.36 Ligand excluded by PLIP POV.26: 15 residues within 4Å: Chain B: I.453, T.456, L.457, Y.460, Y.461 Chain C: I.595, L.599, Y.622, G.623, S.624, F.625, S.626 Ligands: POV.22, POV.23, POV.36 Ligand excluded by PLIP POV.27: 11 residues within 4Å: Chain C: K.435, F.436, H.439, M.440, M.706, W.710, L.711, R.714, F.715 Ligands: FZ4.30, POV.31 Ligand excluded by PLIP POV.28: 20 residues within 4Å: Chain C: S.518, D.519, A.520, W.521, F.522, L.553, L.557, A.560, N.561, L.563, Y.564, R.567, Q.580, I.583, L.584, Q.695 Chain D: F.597, L.664 Ligands: POV.35, POV.36 Ligand excluded by PLIP POV.31: 21 residues within 4Å: Chain C: W.433, K.438, H.439, F.441, F.442, F.445, F.449, W.559, M.562, Y.565, T.566, G.568, F.569, Q.570, R.696 Chain D: F.592, I.595, V.596 Ligands: POV.27, POV.37, POV.38 Ligand excluded by PLIP POV.32: 11 residues within 4Å: Chain C: F.449, F.450, I.453, T.454, L.457, Y.461, L.482, Q.483, G.486 Ligands: POV.37, POV.38 Ligand excluded by PLIP POV.33: 21 residues within 4Å: Chain A: F.592, I.595, V.596 Chain D: W.433, K.438, H.439, F.441, F.442, F.445, F.449, W.559, M.562, Y.565, T.566, G.568, F.569, Q.570, R.696 Ligands: POV.1, POV.3, POV.39 Ligand excluded by PLIP POV.34: 12 residues within 4Å: Chain D: C.446, F.449, F.450, I.453, T.454, L.457, Y.461, L.482, Q.483, G.486 Ligands: POV.1, POV.3 Ligand excluded by PLIP POV.35: 16 residues within 4Å: Chain C: K.545, Y.547, L.548, A.549, V.552, L.553, A.556, A.560 Chain D: V.596, F.597, G.600, F.601, S.607, L.608, Y.650 Ligands: POV.28 Ligand excluded by PLIP POV.36: 17 residues within 4Å: Chain C: I.595, L.599, Y.622, V.629, L.630, F.633 Chain D: K.649, Y.650, P.651, I.652, L.653, F.656, T.660, I.663 Ligands: POV.25, POV.26, POV.28 Ligand excluded by PLIP POV.37: 16 residues within 4Å: Chain C: F.442, F.569, S.571 Chain D: K.581, I.583, L.584, H.585, D.586, V.587, L.588, K.589, F.592, A.675 Ligands: POV.11, POV.31, POV.32 Ligand excluded by PLIP POV.38: 13 residues within 4Å: Chain C: I.453, T.456, L.457, Y.460, Y.461 Chain D: L.599, Y.622, G.623, F.625, S.626 Ligands: POV.11, POV.31, POV.32 Ligand excluded by PLIP POV.39: 11 residues within 4Å: Chain D: K.435, F.436, H.439, M.440, M.706, W.710, L.711, R.714, F.715 Ligands: POV.33, FZ4.42 Ligand excluded by PLIP POV.40: 20 residues within 4Å: Chain A: L.664 Chain D: S.518, D.519, A.520, W.521, F.522, V.525, L.553, L.557, A.560, N.561, L.563, Y.564, R.567, Q.580, I.583, L.584, Q.695 Ligands: POV.10, POV.11 Ligand excluded by PLIP

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

FZ4.6: 8 residues within 4Å: Chain A: H.417, L.420, H.426, L.429, H.430, R.693, L.694, R.696 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.420, A:L.420, A:L.429, A:R.693, A:L.694 FZ4.7: 10 residues within 4Å: Chain A: M.440, S.444, W.493, C.496, I.497, K.500, Y.564, F.703, M.706 Ligands: POV.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.493, A:Y.564, A:F.703 Hydrogen bonds: A:C.496 pi-Stacking: A:F.526 FZ4.20: 8 residues within 4Å: Chain B: H.417, L.420, H.426, L.429, H.430, R.693, L.694, R.696 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.420, B:L.420, B:L.429, B:R.693, B:L.694 FZ4.21: 10 residues within 4Å: Chain B: M.440, S.444, W.493, C.496, I.497, K.500, Y.564, F.703, M.706 Ligands: POV.18 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.493, B:Y.564, B:F.703 Hydrogen bonds: B:C.496 pi-Stacking: B:F.526 FZ4.29: 8 residues within 4Å: Chain C: H.417, L.420, H.426, L.429, H.430, R.693, L.694, R.696 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.420, C:L.420, C:L.429, C:H.430, C:R.693, C:L.694 FZ4.30: 10 residues within 4Å: Chain C: M.440, S.444, W.493, C.496, I.497, K.500, Y.564, F.703, M.706 Ligands: POV.27 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.493, C:Y.564, C:F.703 Hydrogen bonds: C:C.496 pi-Stacking: C:F.526 FZ4.41: 8 residues within 4Å: Chain D: H.417, L.420, H.426, L.429, H.430, R.693, L.694, R.696 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.420, D:L.420, D:L.429, D:H.430, D:R.693, D:L.694 FZ4.42: 10 residues within 4Å: Chain D: M.440, S.444, W.493, C.496, I.497, K.500, Y.564, F.703, M.706 Ligands: POV.39 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:W.493, D:Y.564, D:F.703 Hydrogen bonds: D:C.496

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

NA.12: 1 residues within 4Å: Chain D: G.638 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.638 NA.13: 5 residues within 4Å: Chain A: V.681 Chain B: V.681 Chain C: V.681 Chain D: M.677, V.681 No protein-ligand interaction detected (PLIP) NA.43: 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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