SMTL ID : 9g70.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

5 x ABU: GAMMA-AMINO-BUTANOIC ACID(Non-covalent)

ABU.1: 8 residues within 4Å: Chain A: F.159, E.217, S.218, Y.219, Y.262, T.265 Chain B: R.125, S.189 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.189, A:S.218 Salt bridges: B:R.125 ABU.10: 9 residues within 4Å: Chain A: Y.123, R.125, S.189 Chain E: F.159, E.217, S.218, Y.219, Y.262, T.265 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:Y.123 Hydrogen bonds: A:S.189, E:S.218 Salt bridges: A:R.125 ABU.20: 8 residues within 4Å: Chain B: F.159, E.217, S.218, Y.219, Y.262, T.265 Chain C: R.125, S.189 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.189, B:S.218 Salt bridges: C:R.125 ABU.29: 8 residues within 4Å: Chain C: F.159, E.217, S.218, Y.219, Y.262, T.265 Chain D: R.125, S.189 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.189, C:S.218 Salt bridges: D:R.125 ABU.30: 9 residues within 4Å: Chain D: F.159, E.217, S.218, Y.219, Y.262, T.265 Chain E: R.125, M.177, S.189 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:S.189, D:S.218 Salt bridges: E:R.125

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.11: 1 residues within 4Å: Chain B: N.140 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.140 NAG.12: 2 residues within 4Å: Chain B: N.234, H.254 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:H.254 NAG.21: 1 residues within 4Å: Chain C: N.140 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.140 NAG.22: 2 residues within 4Å: Chain C: N.234, H.254 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:H.254 NAG.31: 1 residues within 4Å: Chain D: N.140 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.140 NAG.32: 2 residues within 4Å: Chain D: N.234, H.254 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:H.254 NAG.39: 1 residues within 4Å: Chain E: N.140 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.140 NAG.40: 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 P9N: Pregnanolone(Non-covalent)

P9N.4: 8 residues within 4Å: Chain A: W.300, V.301, W.304, R.460, P.464 Chain E: L.360, A.363, A.364 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: E:L.360, E:A.363, A:W.300, A:V.301 Hydrogen bonds: A:R.460 P9N.13: 8 residues within 4Å: Chain A: L.360, A.363, A.364 Chain B: W.300, V.301, W.304, R.460, P.464 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.360, A:A.363, B:W.300, B:V.301 Hydrogen bonds: B:R.460 P9N.19: 8 residues within 4Å: Chain B: L.360, A.363, A.364 Chain C: W.300, V.301, W.304, R.460, P.464 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:W.300, C:V.301, B:L.360, B:A.363 Hydrogen bonds: C:R.460 P9N.28: 8 residues within 4Å: Chain C: L.360, A.363, A.364 Chain D: W.300, V.301, W.304, R.460, P.464 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:L.360, C:A.363, D:W.300, D:V.301 Hydrogen bonds: D:R.460 P9N.38: 7 residues within 4Å: Chain D: A.363, Y.367 Chain E: W.300, V.301, W.304, R.460, P.464 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:W.300, E:V.301, D:Y.367, D:Y.367, D:Y.367 Hydrogen bonds: E:R.460

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

OCT.5: 1 residues within 4Å: Chain A: F.290 No protein-ligand interaction detected (PLIP) OCT.6: 2 residues within 4Å: Chain A: Y.458, S.459 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.458, A:Y.458 OCT.14: 1 residues within 4Å: Chain B: F.290 No protein-ligand interaction detected (PLIP) OCT.15: 2 residues within 4Å: Chain B: Y.458, S.459 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.458, B:Y.458 OCT.23: 1 residues within 4Å: Chain C: F.290 No protein-ligand interaction detected (PLIP) OCT.24: 2 residues within 4Å: Chain C: Y.458, S.459 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.458, C:Y.458 OCT.33: 1 residues within 4Å: Chain D: F.290 No protein-ligand interaction detected (PLIP) OCT.34: 2 residues within 4Å: Chain D: Y.458, S.459 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.458, D:Y.458 OCT.41: 1 residues within 4Å: Chain E: F.290 No protein-ligand interaction detected (PLIP) OCT.42: 2 residues within 4Å: Chain E: Y.458, S.459 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:Y.458, E:Y.458

5 x D10: DECANE(Non-covalent)

D10.7: 3 residues within 4Å: Chain A: N.471, L.472, W.475 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.475 D10.16: 3 residues within 4Å: Chain B: N.471, L.472, W.475 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.475 D10.25: 3 residues within 4Å: Chain C: N.471, L.472, W.475 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.475 D10.35: 3 residues within 4Å: Chain D: N.471, L.472, W.475 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.475 D10.43: 3 residues within 4Å: Chain E: N.471, L.472, W.475 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:W.475

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

HEX.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.9: 1 residues within 4Å: Chain A: R.460 No protein-ligand interaction detected (PLIP) HEX.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.18: 1 residues within 4Å: Chain B: R.460 No protein-ligand interaction detected (PLIP) HEX.26: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.27: 1 residues within 4Å: Chain C: R.460 No protein-ligand interaction detected (PLIP) HEX.36: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.37: 1 residues within 4Å: Chain D: R.460 No protein-ligand interaction detected (PLIP) HEX.44: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) HEX.45: 1 residues within 4Å: Chain E: R.460 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.
Show / Hide

Gamma-aminobutyric acid receptor subunit rho-1

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