SMTL ID : 9g5q.1

CryoEM structure of human rho1 GABAA receptor in complex with muscimol in the primed state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

5 x 01: Muscimol

01.1: 10 residues within 4Å: Chain A: F.159, E.217, S.218, Y.219, Y.262, T.265, Y.268 Chain B: R.125, M.177, S.189 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.219 Hydrogen bonds: A:E.217, A:S.218, A:T.265, B:R.125, B:S.189 pi-Stacking: A:Y.262, B:Y.123 01.12: 10 residues within 4Å: Chain B: F.159, E.217, S.218, Y.219, Y.262, T.265, Y.268 Chain C: R.125, M.177, S.189 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:Y.219 Hydrogen bonds: B:E.217, B:S.218, B:T.265, C:R.125, C:S.189 pi-Stacking: B:Y.262, C:Y.123 01.23: 10 residues within 4Å: Chain C: F.159, E.217, S.218, Y.219, Y.262, T.265, Y.268 Chain D: R.125, M.177, S.189 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:Y.219 Hydrogen bonds: C:E.217, C:S.218, C:T.265, D:R.125, D:S.189 pi-Stacking: C:Y.262, D:Y.123 01.34: 10 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, S.189 8 PLIP interactions: 3 interactions with chain E, 5 interactions with chain D Hydrogen bonds: E:R.125, E:S.189, D:E.217, D:S.218, D:T.265 pi-Stacking: E:Y.123, D:Y.262 Hydrophobic interactions: D:Y.219 01.48: 10 residues within 4Å: Chain A: R.125, M.177, S.189 Chain E: F.159, E.217, S.218, Y.219, Y.262, T.265, Y.268 8 PLIP interactions: 5 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: E:Y.219 Hydrogen bonds: E:E.217, E:S.218, E:T.265, A:R.125, A:S.189 pi-Stacking: E:Y.262, A:Y.123

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

NAG.2: 3 residues within 4Å: Chain A: T.138, N.139, N.140 No protein-ligand interaction detected (PLIP) NAG.3: 3 residues within 4Å: Chain A: N.234, H.254, T.255 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.255 NAG.13: 3 residues within 4Å: Chain B: T.138, N.139, N.140 No protein-ligand interaction detected (PLIP) NAG.14: 3 residues within 4Å: Chain B: N.234, H.254, T.255 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.255 NAG.24: 3 residues within 4Å: Chain C: T.138, N.139, N.140 No protein-ligand interaction detected (PLIP) NAG.25: 3 residues within 4Å: Chain C: N.234, H.254, T.255 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.255 NAG.35: 3 residues within 4Å: Chain D: T.138, N.139, N.140 No protein-ligand interaction detected (PLIP) NAG.36: 3 residues within 4Å: Chain D: N.234, H.254, T.255 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.255 NAG.49: 3 residues within 4Å: Chain E: T.138, N.139, N.140 No protein-ligand interaction detected (PLIP) NAG.50: 3 residues within 4Å: Chain E: N.234, H.254, T.255 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.255

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

OCT.4: 2 residues within 4Å: Chain A: L.286, F.290 Ligand excluded by PLIP OCT.7: 3 residues within 4Å: Chain A: Y.458, S.459, I.462 Ligand excluded by PLIP OCT.9: 1 residues within 4Å: Chain A: A.364 Ligand excluded by PLIP OCT.10: 1 residues within 4Å: Chain A: W.349 Ligand excluded by PLIP OCT.11: 3 residues within 4Å: Chain A: F.470, I.473, I.477 Ligand excluded by PLIP OCT.15: 2 residues within 4Å: Chain B: L.286, F.290 Ligand excluded by PLIP OCT.18: 3 residues within 4Å: Chain B: Y.458, S.459, I.462 Ligand excluded by PLIP OCT.20: 1 residues within 4Å: Chain B: A.364 Ligand excluded by PLIP OCT.21: 1 residues within 4Å: Chain B: W.349 Ligand excluded by PLIP OCT.22: 3 residues within 4Å: Chain B: F.470, I.473, I.477 Ligand excluded by PLIP OCT.26: 2 residues within 4Å: Chain C: L.286, F.290 Ligand excluded by PLIP OCT.29: 3 residues within 4Å: Chain C: Y.458, S.459, I.462 Ligand excluded by PLIP OCT.31: 1 residues within 4Å: Chain C: A.364 Ligand excluded by PLIP OCT.32: 1 residues within 4Å: Chain C: W.349 Ligand excluded by PLIP OCT.33: 3 residues within 4Å: Chain C: F.470, I.473, I.477 Ligand excluded by PLIP OCT.37: 2 residues within 4Å: Chain D: L.286, F.290 Ligand excluded by PLIP OCT.40: 3 residues within 4Å: Chain D: Y.458, S.459, I.462 Ligand excluded by PLIP OCT.42: 1 residues within 4Å: Chain D: A.364 Ligand excluded by PLIP OCT.43: 1 residues within 4Å: Chain D: W.349 Ligand excluded by PLIP OCT.44: 3 residues within 4Å: Chain D: F.470, I.473, I.477 Ligand excluded by PLIP OCT.45: 1 residues within 4Å: Chain E: A.364 Ligand excluded by PLIP OCT.46: 1 residues within 4Å: Chain E: W.349 Ligand excluded by PLIP OCT.47: 3 residues within 4Å: Chain E: F.470, I.473, I.477 Ligand excluded by PLIP OCT.51: 2 residues within 4Å: Chain E: L.286, F.290 Ligand excluded by PLIP OCT.54: 3 residues within 4Å: Chain E: Y.458, S.459, I.462 Ligand excluded by PLIP

15 x HEX: HEXANE(Non-covalent)

HEX.5: 1 residues within 4Å: Chain A: W.475 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.475, A:W.475 HEX.6: 2 residues within 4Å: Chain A: W.304, I.461 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.304, A:I.461 HEX.8: 1 residues within 4Å: Chain A: L.357 No protein-ligand interaction detected (PLIP) HEX.16: 1 residues within 4Å: Chain B: W.475 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.475, B:W.475 HEX.17: 2 residues within 4Å: Chain B: W.304, I.461 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.304, B:I.461 HEX.19: 1 residues within 4Å: Chain B: L.357 No protein-ligand interaction detected (PLIP) HEX.27: 1 residues within 4Å: Chain C: W.475 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.475, C:W.475 HEX.28: 2 residues within 4Å: Chain C: W.304, I.461 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.304, C:I.461 HEX.30: 1 residues within 4Å: Chain C: L.357 No protein-ligand interaction detected (PLIP) HEX.38: 1 residues within 4Å: Chain D: W.475 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:W.475, D:W.475 HEX.39: 2 residues within 4Å: Chain D: W.304, I.461 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:W.304, D:I.461 HEX.41: 1 residues within 4Å: Chain D: L.357 No protein-ligand interaction detected (PLIP) HEX.52: 1 residues within 4Å: Chain E: W.475 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:W.475, E:W.475 HEX.53: 2 residues within 4Å: Chain E: W.304, I.461 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:W.304, E:I.461 HEX.55: 1 residues within 4Å: Chain E: L.357 No protein-ligand interaction detected (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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