SMTL ID : 8fc7.1

Cryo-EM structure of the human TRPV4 - RhoA in complex with GSK2798745

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-mer

Ligands

4 x XPW: 1-({(5S,7S)-3-[5-(2-hydroxypropan-2-yl)pyrazin-2-yl]-7-methyl-2-oxo-1-oxa-3-azaspiro[4.5]decan-7-yl}methyl)-1H-benzimidazole-6-carbonitrile(Non-covalent)

XPW.1: 18 residues within 4Å: Chain A: F.471, N.474, S.477, Y.478, L.523, F.524, T.527, N.528, D.531, D.546, F.549, Q.550, Y.553, Y.591, F.592, D.743, I.744, S.747 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.478, A:F.549, A:Q.550, A:Y.553, A:Y.591 XPW.10: 18 residues within 4Å: Chain F: F.471, N.474, S.477, Y.478, L.523, F.524, T.527, N.528, D.531, D.546, F.549, Q.550, Y.553, Y.591, F.592, D.743, I.744, S.747 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:Y.478, F:F.549, F:Q.550, F:Y.553, F:Y.591 XPW.11: 18 residues within 4Å: Chain G: F.471, N.474, S.477, Y.478, L.523, F.524, T.527, N.528, D.531, D.546, F.549, Q.550, Y.553, Y.591, F.592, D.743, I.744, S.747 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:Y.478, G:F.549, G:Q.550, G:Y.553, G:Y.591 XPW.12: 18 residues within 4Å: Chain H: F.471, N.474, S.477, Y.478, L.523, F.524, T.527, N.528, D.531, D.546, F.549, Q.550, Y.553, Y.591, F.592, D.743, I.744, S.747 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:Y.478, H:F.549, H:Q.550, H:Y.553, H:Y.591

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain B: T.19, P.36, T.37, V.38, A.61 Ligands: GDP.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.19, B:T.37 MG.4: 6 residues within 4Å: Chain C: T.19, P.36, T.37, V.38, A.61 Ligands: GDP.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.19, C:T.37 MG.6: 6 residues within 4Å: Chain D: T.19, P.36, T.37, V.38, A.61 Ligands: GDP.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.19, D:T.37 MG.8: 6 residues within 4Å: Chain E: T.19, P.36, T.37, V.38, A.61 Ligands: GDP.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.19, E:T.37

4 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.3: 16 residues within 4Å: Chain B: D.13, G.14, A.15, C.16, G.17, K.18, T.19, C.20, F.30, V.35, K.118, L.121, S.160, A.161, K.162 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:A.15, B:C.16, B:G.17, B:K.18, B:T.19, B:T.19, B:C.20, B:A.161, B:K.162 Salt bridges: B:K.18 pi-Stacking: B:F.30, B:F.30 pi-Cation interactions: B:K.118 GDP.5: 16 residues within 4Å: Chain C: D.13, G.14, A.15, C.16, G.17, K.18, T.19, C.20, F.30, V.35, K.118, L.121, S.160, A.161, K.162 Ligands: MG.4 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:A.15, C:C.16, C:G.17, C:K.18, C:T.19, C:T.19, C:C.20, C:A.161, C:K.162 Salt bridges: C:K.18 pi-Stacking: C:F.30, C:F.30 pi-Cation interactions: C:K.118 GDP.7: 16 residues within 4Å: Chain D: D.13, G.14, A.15, C.16, G.17, K.18, T.19, C.20, F.30, V.35, K.118, L.121, S.160, A.161, K.162 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:A.15, D:C.16, D:G.17, D:K.18, D:T.19, D:T.19, D:C.20, D:A.161, D:K.162 Salt bridges: D:K.18 pi-Stacking: D:F.30, D:F.30 pi-Cation interactions: D:K.118 GDP.9: 16 residues within 4Å: Chain E: D.13, G.14, A.15, C.16, G.17, K.18, T.19, C.20, F.30, V.35, K.118, L.121, S.160, A.161, K.162 Ligands: MG.8 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:A.15, E:C.16, E:G.17, E:K.18, E:T.19, E:T.19, E:C.20, E:A.161, E:K.162 Salt bridges: E:K.18 pi-Stacking: E:F.30, E:F.30 pi-Cation interactions: E: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: AFGH
Transforming protein RhoA: BCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
B

G
C

H
D

B
E

C
F

D
G

E
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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