SMTL ID : 9ff0.1

Cryo-EM structure of the beta3 homomeric GABA(A) receptor in complex with HSM in the short-lived asymmetric open state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

5 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 8 residues within 4Å: Chain A: N.146, R.189, V.191, S.192, R.193, S.206, S.208, R.210 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.189, A:S.206 NAG-NAG-BMA-MAN-MAN.3: 6 residues within 4Å: Chain B: N.146, R.189, V.191, R.193, S.208, R.210 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.189 NAG-NAG-BMA-MAN-MAN.5: 7 residues within 4Å: Chain C: N.146, R.189, V.191, R.193, S.208, F.209, R.210 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.189, C:R.189, C:R.193 NAG-NAG-BMA-MAN-MAN.7: 8 residues within 4Å: Chain D: N.146, R.189, V.191, S.192, R.193, S.206, S.208, R.210 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.189, D:R.193, D:S.206 NAG-NAG-BMA-MAN-MAN.9: 7 residues within 4Å: Chain E: N.146, E.187, R.189, V.191, R.193, S.208, R.210 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.189, E:R.189

5 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 2 residues within 4Å: Chain A: N.77, H.116 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain B: N.77, H.116 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain C: N.77, H.116 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain D: Y.63, N.77, H.116 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain E: N.77, H.116 No protein-ligand interaction detected (PLIP)

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

NAG.11: 3 residues within 4Å: Chain A: D.2, N.5, S.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.5, A:S.7 NAG.14: 4 residues within 4Å: Chain B: N.1, N.5, S.7, E.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.1, B:F.8, B:E.11 NAG.16: 4 residues within 4Å: Chain C: N.5, S.7, F.8, E.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.11 NAG.18: 4 residues within 4Å: Chain D: N.5, S.7, F.8, E.11 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.1, D:S.7, D:S.7 NAG.20: 3 residues within 4Å: Chain E: N.5, S.7, E.11 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.7, E:E.11

5 x HSM: HISTAMINE(Non-covalent)

HSM.12: 8 residues within 4Å: Chain A: Y.94, E.152, S.153, Y.154, F.197, Y.202 Chain B: D.40, Y.59 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.202 Hydrogen bonds: A:Y.94, A:E.152, B:D.40 pi-Stacking: A:F.197 HSM.13: 8 residues within 4Å: Chain B: Y.94, E.152, S.153, Y.154, F.197, Y.202 Chain C: D.40, Y.59 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:Y.94, B:E.152, C:D.40, C:Q.61 pi-Stacking: C:Y.59 HSM.15: 10 residues within 4Å: Chain C: Y.94, E.152, S.153, Y.154, F.197, T.199, Y.202 Chain D: D.40, Y.59, Q.61 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Y.94, C:E.152, D:D.40, D:Q.61 pi-Stacking: C:F.197, D:Y.59 HSM.17: 7 residues within 4Å: Chain D: Y.94, E.152, Y.154, F.197, Y.202 Chain E: D.40, Q.61 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:D.40, E:Q.61, D:Y.94, D:E.152 pi-Stacking: E:Y.59 HSM.19: 8 residues within 4Å: Chain A: D.40, Y.59, Q.61 Chain E: Y.94, E.152, Y.154, F.197, Y.202 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain A Hydrogen bonds: E:Y.94, E:E.152, A:D.40, A:Q.61 pi-Stacking: E:F.197, A:Y.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mihaylov, D.B. et al., Cryo-EM structure of the beta3 homomeric GABA(A) receptor in complex with HSM in the short-lived asymmetric open state. To Be Published

Release Date

2025-06-11

Peptides

Gamma-aminobutyric acid receptor subunit beta-3: 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 beta-3