SMTL ID : 7qne.1

Cryo-EM structure of human full-length synaptic alpha1beta3gamma2 GABA(A)R in complex with Ro15-4513 and megabody Mb38

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN-MAN.1: 14 residues within 4Å: Chain A: N.138, T.140 Chain C: S.139, N.140, V.142, G.143, K.144, D.159, W.162, P.166 Chain D: N.55, S.119, A.136 Ligands: NAG-NAG-BMA-MAN-MAN.4 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.159

2 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: 3 residues within 4Å: Chain B: P.103, N.105, H.144 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain E: P.103, N.105, H.144 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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-MAN.3: 9 residues within 4Å: Chain B: N.174, R.217, V.219, S.220, R.221, S.234, S.236, F.237, R.238 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.234 NAG-NAG-BMA-MAN-MAN-MAN.6: 10 residues within 4Å: Chain E: N.174, T.176, R.217, V.219, S.220, R.221, N.222, S.234, S.236, R.238 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.234

1 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.4: 6 residues within 4Å: Chain A: L.116 Chain D: N.138, M.141, P.142 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.1 No protein-ligand interaction detected (PLIP)

2 x PIO: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate(Non-covalent)

PIO.7: 13 residues within 4Å: Chain A: R.276, E.330, T.333, F.337, K.339, R.340, N.414, S.415, S.417, K.418, I.419, L.422, S.423 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.419, A:I.419, A:L.422 Hydrogen bonds: A:R.276, A:R.276, A:F.337, A:N.414, A:S.415, A:K.418 Salt bridges: A:R.276, A:K.339, A:K.339, A:R.340, A:K.418, A:K.418 PIO.17: 11 residues within 4Å: Chain D: R.276, T.333, F.337, K.339, R.340, N.414, S.415, S.417, K.418, I.419, L.422 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:I.419, D:L.422 Hydrogen bonds: D:R.276, D:F.337, D:S.415, D:V.416, D:K.418, D:I.419 Salt bridges: D:R.276, D:K.339, D:K.339, D:R.340, D:K.418, D:K.418

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

OCT.8: 3 residues within 4Å: Chain A: I.250, I.262, W.439 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.250, A:I.262, A:W.439

4 x D10: DECANE(Non-covalent)

D10.9: 6 residues within 4Å: Chain A: I.266, Q.269, V.270, W.273 Chain B: F.326, Y.329 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.326, B:F.326, B:Y.329, A:I.266, A:W.273, A:W.273, A:W.273, A:W.273 D10.11: 7 residues within 4Å: Chain B: W.262, V.263, W.266, P.457 Chain C: G.354, T.355, Y.358 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:W.262, B:V.263, B:W.266, B:W.266, B:W.266, B:P.457, C:Y.358 D10.13: 5 residues within 4Å: Chain C: V.288, W.291, W.295 Chain D: A.332, Y.336 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:V.288, C:W.291, C:W.295, C:W.295, D:A.332, D:Y.336 D10.18: 3 residues within 4Å: Chain A: A.332, Y.336 Chain E: W.266 7 PLIP interactions: 4 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: E:W.266, E:W.266, E:W.266, E:W.266, A:A.332, A:Y.336, A:Y.336

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 4 residues within 4Å: Chain A: V.80, L.215, N.216, Q.217 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain C: P.103, V.104, L.237, Y.238, Q.239, F.240 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain D: V.80, N.216, Q.217, Y.218 Ligand excluded by PLIP

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

NAG.14: 5 residues within 4Å: Chain C: W.222, R.224, N.247, T.248, T.249 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.224

1 x EIE: ethyl 8-[(azanylidene-$l^{4}-azanylidene)amino]-5-methyl-6-oxidanylidene-4~{H}-imidazo[1,5-a][1,4]benzodiazepine-3-carboxylate(Non-covalent)

EIE.16: 15 residues within 4Å: Chain C: M.96, Y.97, F.116, A.118, T.181 Chain D: F.127, H.129, G.185, S.186, Y.187, S.232, S.233, T.234, Y.237, V.238 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:F.127, C:Y.97, C:A.118 Hydrogen bonds: D:S.186, D:S.232 pi-Stacking: D:Y.237, C:F.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sente, A. et al., Differential assembly diversifies GABA A receptor structures and signalling. Nature (2022)

Release Date

2022-04-13

Peptides

GABA(A) receptor subunit alpha-1: AD
Gamma-aminobutyric acid receptor subunit beta-3: BE
GABA(A) receptor subunit gamma-2: C
Megabody Mb38: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
G

Membrane

We predict this structure to be a membrane protein.
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GABA(A) receptor subunit alpha-1

Gamma-aminobutyric acid receptor subunit beta-3

GABA(A) receptor subunit gamma-2

Megabody Mb38

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