SMTL ID : 9g78.1

CryoEM structure of human rho1 GABAA receptor in complex with neurosteroid pregnanolone

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

10 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.1: 1 residues within 4Å: Chain A: N.140 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.140 NAG.2: 2 residues within 4Å: Chain A: N.234, H.254 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.234, A:T.255 NAG.15: 1 residues within 4Å: Chain B: N.140 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.140 NAG.16: 2 residues within 4Å: Chain B: N.234, H.254 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.234, B:T.255 NAG.27: 1 residues within 4Å: Chain C: N.140 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.140 NAG.28: 2 residues within 4Å: Chain C: N.234, H.254 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.234, C:T.255 NAG.39: 1 residues within 4Å: Chain D: N.140 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.140 NAG.40: 2 residues within 4Å: Chain D: N.234, H.254 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.234, D:T.255 NAG.51: 1 residues within 4Å: Chain E: N.140 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.140 NAG.52: 2 residues within 4Å: Chain E: N.234, H.254 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.234, E:T.255

5 x P9N: Pregnanolone(Non-covalent)

P9N.3: 7 residues within 4Å: Chain A: W.300, W.304, R.460, P.464 Chain E: A.363, A.364, Y.367 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:W.300, A:W.304, A:W.304, A:W.304, E:Y.367, E:Y.367 Hydrogen bonds: A:R.460 P9N.12: 7 residues within 4Å: Chain A: A.363, A.364, Y.367 Chain B: W.300, W.304, R.460, P.464 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.300, B:W.304, B:W.304, B:W.304, A:A.363, A:Y.367, A:Y.367 Hydrogen bonds: B:R.460 P9N.25: 7 residues within 4Å: Chain B: A.363, A.364, Y.367 Chain C: W.300, W.304, R.460, P.464 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:W.300, C:W.304, C:W.304, C:W.304, B:Y.367, B:Y.367 Hydrogen bonds: C:R.460 P9N.37: 6 residues within 4Å: Chain C: A.364, Y.367 Chain D: W.300, W.304, R.460, P.464 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:W.300, D:W.304, D:W.304, D:W.304, C:A.364, C:Y.367 Hydrogen bonds: D:R.460 P9N.49: 7 residues within 4Å: Chain D: A.363, A.364, Y.367 Chain E: W.300, W.304, R.460, P.464 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:W.300, E:W.304, E:W.304, E:W.304, D:Y.367, D:Y.367 Hydrogen bonds: E:R.460

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

OCT.4: 3 residues within 4Å: Chain A: W.304 Chain E: Y.367 Ligands: D10.9 Ligand excluded by PLIP OCT.7: 2 residues within 4Å: Chain A: S.479 Ligands: OCT.13 Ligand excluded by PLIP OCT.8: 2 residues within 4Å: Chain A: L.472, W.475 Ligand excluded by PLIP OCT.13: 4 residues within 4Å: Chain A: L.286, Y.289, T.293 Ligands: OCT.7 Ligand excluded by PLIP OCT.14: 3 residues within 4Å: Chain B: T.293, Y.347 Ligands: OCT.20 Ligand excluded by PLIP OCT.17: 3 residues within 4Å: Chain A: Y.367 Chain B: W.304 Ligands: D10.22 Ligand excluded by PLIP OCT.20: 2 residues within 4Å: Chain B: S.479 Ligands: OCT.14 Ligand excluded by PLIP OCT.21: 2 residues within 4Å: Chain B: L.472, W.475 Ligand excluded by PLIP OCT.26: 4 residues within 4Å: Chain C: L.286, Y.289, T.293 Ligands: OCT.32 Ligand excluded by PLIP OCT.29: 3 residues within 4Å: Chain B: Y.367 Chain C: W.304 Ligands: D10.34 Ligand excluded by PLIP OCT.32: 2 residues within 4Å: Chain C: S.479 Ligands: OCT.26 Ligand excluded by PLIP OCT.33: 2 residues within 4Å: Chain C: L.472, W.475 Ligand excluded by PLIP OCT.38: 4 residues within 4Å: Chain D: L.286, Y.289, T.293, Y.347 Ligand excluded by PLIP OCT.41: 3 residues within 4Å: Chain C: Y.367 Chain D: W.304 Ligands: D10.46 Ligand excluded by PLIP OCT.44: 1 residues within 4Å: Chain D: S.479 Ligand excluded by PLIP OCT.45: 2 residues within 4Å: Chain D: L.472, W.475 Ligand excluded by PLIP OCT.50: 5 residues within 4Å: Chain E: L.286, Y.289, T.293, Y.347 Ligands: OCT.56 Ligand excluded by PLIP OCT.53: 3 residues within 4Å: Chain D: Y.367 Chain E: W.304 Ligands: D10.58 Ligand excluded by PLIP OCT.56: 2 residues within 4Å: Chain E: S.479 Ligands: OCT.50 Ligand excluded by PLIP OCT.57: 2 residues within 4Å: Chain E: L.472, W.475 Ligand excluded by PLIP

5 x D12: DODECANE(Non-covalent)

D12.5: 5 residues within 4Å: Chain A: L.357, Y.458, S.459, I.462, F.463 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.357, A:Y.458, A:Y.458, A:I.462, A:F.463 D12.18: 5 residues within 4Å: Chain B: L.357, Y.458, S.459, I.462, F.463 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.357, B:Y.458, B:Y.458, B:I.462, B:F.463 D12.30: 5 residues within 4Å: Chain C: L.357, Y.458, S.459, I.462, F.463 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.357, C:Y.458, C:Y.458, C:I.462, C:F.463 D12.42: 5 residues within 4Å: Chain D: L.357, Y.458, S.459, I.462, F.463 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.357, D:Y.458, D:Y.458, D:I.462, D:F.463 D12.54: 5 residues within 4Å: Chain E: L.357, Y.458, S.459, I.462, F.463 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:L.357, E:Y.458, E:Y.458, E:I.462, E:F.463

10 x D10: DECANE(Non-functional Binders)(Non-covalent)

D10.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D10.9: 3 residues within 4Å: Chain A: W.304, I.461 Ligands: OCT.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.304 D10.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D10.22: 3 residues within 4Å: Chain B: W.304, I.461 Ligands: OCT.17 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.304 D10.31: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D10.34: 3 residues within 4Å: Chain C: W.304, I.461 Ligands: OCT.29 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.304 D10.43: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D10.46: 3 residues within 4Å: Chain D: W.304, I.461 Ligands: OCT.41 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.304 D10.55: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) D10.58: 3 residues within 4Å: Chain E: W.304, I.461 Ligands: OCT.53 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:W.304

10 x HEX: HEXANE(Non-covalent)

HEX.10: 2 residues within 4Å: Chain A: I.346, W.349 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.346, A:W.349 HEX.11: 2 residues within 4Å: Chain A: L.357, A.364 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.364 HEX.23: 2 residues within 4Å: Chain B: I.346, W.349 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.346, B:W.349 HEX.24: 2 residues within 4Å: Chain B: L.357, A.364 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.364 HEX.35: 2 residues within 4Å: Chain C: I.346, W.349 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.346, C:W.349 HEX.36: 2 residues within 4Å: Chain C: L.357, A.364 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.364 HEX.47: 2 residues within 4Å: Chain D: I.346, W.349 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.346, D:W.349 HEX.48: 2 residues within 4Å: Chain D: L.357, A.364 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:A.364 HEX.59: 2 residues within 4Å: Chain E: I.346, W.349 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:I.346, E:W.349 HEX.60: 2 residues within 4Å: Chain E: L.357, A.364 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:A.364

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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