SMTL ID : 8fcb.1

Cryo-EM structure of the human TRPV4 - RhoA in complex with GSK1016790A

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.52 Å

Oligo State

hetero-4-4-mer

Ligands

4 x XQ3: N-[(2S)-1-{4-[N-(2,4-dichlorobenzene-1-sulfonyl)-L-seryl]piperazin-1-yl}-4-methyl-1-oxopentan-2-yl]-1-benzothiophene-2-carboxamide(Non-covalent)

XQ3.1: 21 residues within 4Å: Chain A: S.470, N.474, S.477, Y.478, A.481, T.520, L.523, F.524, T.527, N.528, D.531, K.535, F.549, Q.550, Y.553, Y.591, F.592, D.743, I.744, S.747, F.748 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.520, A:F.524, A:Y.553, A:Y.591, A:F.592, A:F.748 Hydrogen bonds: A:N.474, A:N.474, A:N.528, A:D.531 Halogen bonds: A:F.524 XQ3.2: 21 residues within 4Å: Chain B: S.470, N.474, S.477, Y.478, A.481, T.520, L.523, F.524, T.527, N.528, D.531, K.535, F.549, Q.550, Y.553, Y.591, F.592, D.743, I.744, S.747, F.748 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:T.520, B:F.524, B:Y.553, B:Y.591, B:F.592, B:F.748 Hydrogen bonds: B:N.474, B:N.474, B:N.528, B:D.531 Halogen bonds: B:F.524 XQ3.5: 21 residues within 4Å: Chain C: S.470, N.474, S.477, Y.478, A.481, T.520, L.523, F.524, T.527, N.528, D.531, K.535, F.549, Q.550, Y.553, Y.591, F.592, D.743, I.744, S.747, F.748 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:T.520, C:F.524, C:Y.553, C:Y.591, C:F.592, C:F.748 Hydrogen bonds: C:N.474, C:N.474, C:N.528, C:D.531 Halogen bonds: C:F.524 XQ3.7: 21 residues within 4Å: Chain D: S.470, N.474, S.477, Y.478, A.481, T.520, L.523, F.524, T.527, N.528, D.531, K.535, F.549, Q.550, Y.553, Y.591, F.592, D.743, I.744, S.747, F.748 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:T.520, D:F.524, D:Y.553, D:Y.591, D:F.592, D:F.748 Hydrogen bonds: D:N.474, D:N.474, D:N.528, D:D.531 Halogen bonds: D:F.524

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.3: 14 residues within 4Å: Chain B: V.693, I.696, I.697, V.700, I.704 Chain D: L.618, Y.621, L.622, M.625, S.667, T.668, L.670, L.671, F.674 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:V.693, B:I.696, B:V.700, B:V.700, B:I.704, D:Y.621, D:F.674, D:F.674 Y01.4: 15 residues within 4Å: Chain A: V.693, I.696, I.697, V.700, I.704 Chain C: L.618, Y.621, L.622, M.625, E.664, S.667, T.668, L.670, L.671, F.674 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.693, A:I.696, A:V.700, A:V.700, A:I.704, C:Y.621 Y01.6: 15 residues within 4Å: Chain B: L.618, Y.621, L.622, M.625, E.664, S.667, T.668, L.670, L.671, F.674 Chain C: V.693, I.696, I.697, V.700, I.704 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:Y.621, B:F.674, B:F.674, C:V.693, C:I.696, C:V.700, C:V.700, C:I.704 Y01.8: 15 residues within 4Å: Chain A: L.618, Y.621, L.622, M.625, E.664, S.667, T.668, L.670, L.671, F.674 Chain D: V.693, I.696, I.697, V.700, I.704 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:V.693, D:I.696, D:V.700, D:V.700, D:I.704, A:Y.621, A:L.670, A:F.674

4 x GSP: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE(Covalent)

GSP.9: 16 residues within 4Å: Chain E: G.14, A.15, C.16, G.17, K.18, T.19, C.20, F.30, V.35, T.37, A.61, Q.63, K.118, L.121, A.161, K.162 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:C.16, E:G.17, E:K.18, E:K.18, E:K.18, E:K.118, E:A.161, E:K.162, E:K.162 pi-Cation interactions: E:K.118 GSP.10: 16 residues within 4Å: Chain F: G.14, A.15, C.16, G.17, K.18, T.19, C.20, F.30, V.35, T.37, A.61, Q.63, K.118, L.121, A.161, K.162 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:C.16, F:G.17, F:K.18, F:K.18, F:K.18, F:K.118, F:A.161, F:K.162, F:K.162 pi-Cation interactions: F:K.118 GSP.11: 16 residues within 4Å: Chain G: G.14, A.15, C.16, G.17, K.18, T.19, C.20, F.30, V.35, T.37, A.61, Q.63, K.118, L.121, A.161, K.162 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:C.16, G:G.17, G:K.18, G:K.18, G:K.18, G:K.118, G:A.161, G:K.162, G:K.162 pi-Cation interactions: G:K.118 GSP.12: 16 residues within 4Å: Chain H: G.14, A.15, C.16, G.17, K.18, T.19, C.20, F.30, V.35, T.37, A.61, Q.63, K.118, L.121, A.161, K.162 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:C.16, H:G.17, H:K.18, H:K.18, H:K.18, H:K.118, H:A.161, H:K.162, H:K.162 pi-Cation interactions: H:K.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kwon, D.H. et al., TRPV4-Rho GTPase complex structures reveal mechanisms of gating and disease. Nat Commun (2023)

Release Date

2023-07-12

Peptides

Transient receptor potential cation channel subfamily V member 4: ABCD
Transforming protein RhoA: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Membrane

We predict this structure to be a membrane protein.
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Transient receptor potential cation channel subfamily V member 4

Transforming protein RhoA

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