SMTL ID : 9g62.1

CryoEM structure of human rho1 GABAA receptor in complex with muscimol and neurosteroid THDOC in the desensitized state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

5 x 01: Muscimol

01.1: 8 residues within 4Å: Chain A: F.159, E.217, S.218, Y.219, Y.262, T.265, Y.268 Chain B: R.125 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.262 Hydrogen bonds: A:E.217, A:Y.219, A:T.265, A:Y.268, B:R.125 pi-Stacking: A:Y.219 01.11: 8 residues within 4Å: Chain B: F.159, E.217, S.218, Y.219, Y.262, T.265, Y.268 Chain C: R.125 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Y.262 Hydrogen bonds: B:E.217, B:Y.219, B:T.265, B:Y.268, C:R.125 pi-Stacking: B:Y.219 01.21: 8 residues within 4Å: Chain C: F.159, E.217, S.218, Y.219, Y.262, T.265, Y.268 Chain D: R.125 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Y.262 Hydrogen bonds: C:E.217, C:Y.219, C:T.265, C:Y.268, D:R.125 pi-Stacking: C:Y.219 01.31: 9 residues within 4Å: Chain D: F.159, E.217, S.218, Y.219, Y.262, T.265, Y.268 Chain E: R.125, M.177 7 PLIP interactions: 1 interactions with chain E, 6 interactions with chain D Hydrogen bonds: E:R.125, D:E.217, D:Y.219, D:T.265, D:Y.268 Hydrophobic interactions: D:Y.262 pi-Stacking: D:Y.219 01.42: 9 residues within 4Å: Chain A: Y.123, R.125 Chain E: F.159, E.217, S.218, Y.219, Y.262, T.265, Y.268 8 PLIP interactions: 6 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:Y.262, A:Y.123 Hydrogen bonds: E:E.217, E:Y.219, E:T.265, E:Y.268, A:R.125 pi-Stacking: E:Y.219

10 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 1 residues within 4Å: Chain A: N.140 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.140 NAG.3: 2 residues within 4Å: Chain A: N.234, H.254 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:H.254 NAG.12: 1 residues within 4Å: Chain B: N.140 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.140 NAG.13: 2 residues within 4Å: Chain B: N.234, H.254 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:H.254 NAG.22: 1 residues within 4Å: Chain C: N.140 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.140 NAG.23: 2 residues within 4Å: Chain C: N.234, H.254 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:H.254 NAG.32: 1 residues within 4Å: Chain D: N.140 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.140 NAG.33: 2 residues within 4Å: Chain D: N.234, H.254 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:H.254 NAG.43: 1 residues within 4Å: Chain E: N.140 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.140 NAG.44: 2 residues within 4Å: Chain E: N.234, H.254 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:H.254

5 x A8Z: Tetrahydrodeoxycorticosterone(Non-covalent)

A8Z.4: 6 residues within 4Å: Chain A: L.285, T.293, Y.347, N.471, W.475 Ligands: D12.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.285, A:L.285, A:W.475, A:W.475, A:W.475 Hydrogen bonds: A:T.293, A:T.293, A:N.471 A8Z.14: 6 residues within 4Å: Chain B: L.285, T.293, Y.347, N.471, W.475 Ligands: D12.15 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.285, B:L.285, B:W.475, B:W.475, B:W.475 Hydrogen bonds: B:T.293, B:T.293, B:N.471 A8Z.24: 6 residues within 4Å: Chain C: L.285, T.293, Y.347, N.471, W.475 Ligands: D12.25 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.285, C:L.285, C:W.475, C:W.475, C:W.475 Hydrogen bonds: C:T.293, C:T.293, C:N.471 A8Z.34: 6 residues within 4Å: Chain D: L.285, T.293, Y.347, N.471, W.475 Ligands: D12.35 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.285, D:L.285, D:W.475, D:W.475, D:W.475 Hydrogen bonds: D:T.293, D:T.293, D:N.471 A8Z.45: 6 residues within 4Å: Chain E: L.285, T.293, Y.347, N.471, W.475 Ligands: D12.46 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:L.285, E:L.285, E:W.475, E:W.475, E:W.475 Hydrogen bonds: E:T.293, E:T.293, E:N.471

5 x D12: DODECANE(Non-covalent)

D12.5: 4 residues within 4Å: Chain A: T.293, Y.467, L.472 Ligands: A8Z.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.293, A:Y.467 D12.15: 4 residues within 4Å: Chain B: T.293, Y.467, L.472 Ligands: A8Z.14 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.293, B:Y.467 D12.25: 4 residues within 4Å: Chain C: T.293, Y.467, L.472 Ligands: A8Z.24 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:T.293, C:Y.467 D12.35: 4 residues within 4Å: Chain D: T.293, Y.467, L.472 Ligands: A8Z.34 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:T.293, D:Y.467 D12.46: 4 residues within 4Å: Chain E: T.293, Y.467, L.472 Ligands: A8Z.45 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:T.293, E:Y.467

5 x OCT: N-OCTANE(Non-covalent)

OCT.6: 3 residues within 4Å: Chain A: V.301, W.304 Chain E: A.364 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:A.364, A:V.301, A:W.304 OCT.16: 3 residues within 4Å: Chain A: A.364 Chain B: V.301, W.304 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.301, B:W.304, A:A.364 OCT.26: 3 residues within 4Å: Chain B: A.364 Chain C: V.301, W.304 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:V.301, C:W.304, B:A.364 OCT.36: 3 residues within 4Å: Chain C: A.364 Chain D: V.301, W.304 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:A.364, D:V.301, D:W.304 OCT.41: 3 residues within 4Å: Chain D: Y.367 Chain E: V.301, W.304 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:Y.367, E:V.301, E:W.304

20 x HEX: HEXANE(Non-covalent)(Non-functional Binders)

HEX.7: 2 residues within 4Å: Chain A: Y.458, S.459 Ligand excluded by PLIP HEX.8: 1 residues within 4Å: Chain A: I.477 Ligand excluded by PLIP HEX.9: 2 residues within 4Å: Chain A: W.304, I.461 Ligand excluded by PLIP HEX.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP HEX.17: 2 residues within 4Å: Chain B: Y.458, S.459 Ligand excluded by PLIP HEX.18: 1 residues within 4Å: Chain B: I.477 Ligand excluded by PLIP HEX.19: 2 residues within 4Å: Chain B: W.304, I.461 Ligand excluded by PLIP HEX.20: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP HEX.27: 2 residues within 4Å: Chain C: Y.458, S.459 Ligand excluded by PLIP HEX.28: 1 residues within 4Å: Chain C: I.477 Ligand excluded by PLIP HEX.29: 2 residues within 4Å: Chain C: W.304, I.461 Ligand excluded by PLIP HEX.30: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP HEX.37: 2 residues within 4Å: Chain D: Y.458, S.459 Ligand excluded by PLIP HEX.38: 1 residues within 4Å: Chain D: I.477 Ligand excluded by PLIP HEX.39: 2 residues within 4Å: Chain D: W.304, I.461 Ligand excluded by PLIP HEX.40: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP HEX.47: 2 residues within 4Å: Chain E: Y.458, S.459 Ligand excluded by PLIP HEX.48: 1 residues within 4Å: Chain E: I.477 Ligand excluded by PLIP HEX.49: 2 residues within 4Å: Chain E: W.304, I.461 Ligand excluded by PLIP HEX.50: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fan, C. et al., CryoEM structure of human rho1 GABAA receptor in complex with neurosteroid. To be published

Release Date

2025-07-30

Peptides

Gamma-aminobutyric acid receptor subunit rho-1: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Gamma-aminobutyric acid receptor subunit rho-1

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