SMTL ID : 6uw4.1

Cryo-EM structure of human TRPV3 determined in lipid nanodisc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

20 x 6OU: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate(Non-covalent)

6OU.1: 12 residues within 4Å: Chain A: M.440, S.444, W.493, C.496, K.500, E.501, H.523, F.526, Y.564, Y.565, F.703, M.706 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.500 Hydrogen bonds: A:S.444, A:S.444, A:H.523 Salt bridges: A:K.500, A:K.500 6OU.2: 7 residues within 4Å: Chain A: A.549, C.550 Chain D: Y.650, P.651, I.652, L.653, F.656 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.653, D:F.656 6OU.3: 14 residues within 4Å: Chain A: L.591, Y.594, I.595, S.626, V.629, F.633, I.637 Chain D: I.644, Q.645, I.652, L.655, I.663, F.666, V.667 11 PLIP interactions: 6 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:L.655, D:I.663, D:I.663, D:F.666, D:V.667, A:L.591, A:I.595, A:V.629, A:F.633, A:I.637 Hydrogen bonds: D:Q.645 6OU.4: 8 residues within 4Å: Chain A: L.599, V.603, S.624, F.625, S.626 Chain B: Y.460, Y.461, W.559 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.599, A:L.599, A:V.603, A:F.625, B:W.559, B:W.559 Hydrogen bonds: A:S.624, A:S.626 6OU.5: 7 residues within 4Å: Chain A: S.571, M.572, M.574 Chain D: L.584, H.585, L.588, K.589 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.588 Salt bridges: D:H.585, D:K.589 6OU.7: 12 residues within 4Å: Chain B: M.440, S.444, W.493, C.496, K.500, E.501, H.523, F.526, Y.564, Y.565, F.703, M.706 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:K.500 Hydrogen bonds: B:S.444, B:S.444, B:H.523 Salt bridges: B:K.500, B:K.500 6OU.8: 7 residues within 4Å: Chain A: Y.650, P.651, I.652, L.653, F.656 Chain B: A.549, C.550 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.653, A:F.656 6OU.9: 14 residues within 4Å: Chain A: I.644, Q.645, I.652, L.655, I.663, F.666, V.667 Chain B: L.591, Y.594, I.595, S.626, V.629, F.633, I.637 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.655, A:I.663, A:I.663, A:F.666, A:V.667, B:L.591, B:I.595, B:V.629, B:F.633, B:I.637 Hydrogen bonds: A:Q.645 6OU.10: 8 residues within 4Å: Chain B: L.599, V.603, S.624, F.625, S.626 Chain C: Y.460, Y.461, W.559 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.599, B:L.599, B:V.603, B:F.625, C:W.559, C:W.559 Hydrogen bonds: B:S.624, B:S.626 6OU.11: 7 residues within 4Å: Chain A: L.584, H.585, L.588, K.589 Chain B: S.571, M.572, M.574 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.588 Salt bridges: A:H.585, A:K.589 6OU.12: 12 residues within 4Å: Chain C: M.440, S.444, W.493, C.496, K.500, E.501, H.523, F.526, Y.564, Y.565, F.703, M.706 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:K.500 Hydrogen bonds: C:S.444, C:S.444, C:H.523 Salt bridges: C:K.500, C:K.500 6OU.13: 7 residues within 4Å: Chain B: Y.650, P.651, I.652, L.653, F.656 Chain C: A.549, C.550 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.653, B:F.656 6OU.14: 14 residues within 4Å: Chain B: I.644, Q.645, I.652, L.655, I.663, F.666, V.667 Chain C: L.591, Y.594, I.595, S.626, V.629, F.633, I.637 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:L.655, B:I.663, B:I.663, B:F.666, B:V.667, C:L.591, C:I.595, C:V.629, C:F.633, C:I.637 Hydrogen bonds: B:Q.645 6OU.15: 8 residues within 4Å: Chain C: L.599, V.603, S.624, F.625, S.626 Chain D: Y.460, Y.461, W.559 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.599, C:L.599, C:V.603, C:F.625, D:W.559, D:W.559 Hydrogen bonds: C:S.624, C:S.626 6OU.16: 7 residues within 4Å: Chain B: L.584, H.585, L.588, K.589 Chain C: S.571, M.572, M.574 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.588 Salt bridges: B:H.585, B:K.589 6OU.17: 12 residues within 4Å: Chain D: M.440, S.444, W.493, C.496, K.500, E.501, H.523, F.526, Y.564, Y.565, F.703, M.706 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:K.500 Hydrogen bonds: D:S.444, D:S.444, D:H.523 Salt bridges: D:K.500, D:K.500 6OU.18: 7 residues within 4Å: Chain C: Y.650, P.651, I.652, L.653, F.656 Chain D: A.549, C.550 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.653, C:F.656 6OU.19: 14 residues within 4Å: Chain C: I.644, Q.645, I.652, L.655, I.663, F.666, V.667 Chain D: L.591, Y.594, I.595, S.626, V.629, F.633, I.637 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:L.655, C:I.663, C:I.663, C:F.666, C:V.667, D:L.591, D:I.595, D:V.629, D:F.633, D:I.637 Hydrogen bonds: C:Q.645 6OU.20: 8 residues within 4Å: Chain A: Y.460, Y.461, W.559 Chain D: L.599, V.603, S.624, F.625, S.626 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:L.599, D:L.599, D:V.603, D:F.625, A:W.559, A:W.559 Hydrogen bonds: D:S.624, D:S.626 6OU.21: 7 residues within 4Å: Chain C: L.584, H.585, L.588, K.589 Chain D: S.571, M.572, M.574 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.588 Salt bridges: C:H.585, C:K.589

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

NA.6: 4 residues within 4Å: Chain A: G.638 Chain B: G.638 Chain C: G.638 Chain D: G.638 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.638

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deng, Z. et al., Gating of human TRPV3 in a lipid bilayer. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-07-01

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