SMTL ID : 6i53.1

Cryo-EM structure of the human synaptic alpha1-beta3-gamma2 GABAA receptor in complex with Megabody38 in a lipid nanodisc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-1-mer

Ligands

2 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.174, R.217, V.219, S.220, R.221, S.236, F.237, R.238 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.217 NAG-NAG-BMA-MAN-MAN.7: 7 residues within 4Å: Chain A: D.114, Q.115 Chain E: N.146, M.149, P.150 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.3, NAG-NAG-BMA-MAN-MAN-MAN-MAN.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.115, A:D.114

3 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 A: P.103, N.105, H.144 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain C: N.105, H.144 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain D: R.224, S.226, N.247 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.3: 5 residues within 4Å: Chain B: N.146, T.148 Chain C: K.137 Chain D: W.162 Ligands: NAG-NAG-BMA-MAN-MAN.7 No protein-ligand interaction detected (PLIP)

1 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.4: 8 residues within 4Å: Chain C: N.174, R.217, V.219, S.220, R.221, S.236, F.237, R.238 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.217, C:R.217, C:R.221

3 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.8: 7 residues within 4Å: Chain A: I.243, I.247, I.255, S.461, N.464, W.468, V.472 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.255, A:W.468 POV.10: 8 residues within 4Å: Chain B: I.258, G.259, I.263, N.443, W.447 Chain C: P.301, V.303, M.311 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:V.303, B:I.263, B:W.447 POV.12: 6 residues within 4Å: Chain A: P.301, V.303 Chain E: K.257, I.258, G.259, L.267 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:L.267, A:V.303 Hydrogen bonds: E:I.258, E:G.259

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.9: 11 residues within 4Å: Chain B: R.284, T.341, F.345, K.347, R.348, N.422, S.423, S.425, K.426, I.427, L.430 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:T.341, B:I.427, B:I.427, B:L.430 Hydrogen bonds: B:R.284, B:R.284, B:N.422, B:S.423, B:K.426 Salt bridges: B:R.284, B:K.347, B:K.347, B:R.348, B:K.426, B:K.426 PIO.11: 11 residues within 4Å: Chain E: R.284, T.341, F.345, K.347, R.348, N.422, S.423, S.425, K.426, I.427, L.430 18 PLIP interactions: 18 interactions with chain E Hydrophobic interactions: E:T.341, E:F.345, E:I.427, E:I.427, E:L.430 Hydrogen bonds: E:R.284, E:R.284, E:S.423, E:S.423, E:S.423, E:K.426, E:I.427 Salt bridges: E:R.284, E:K.347, E:K.347, E:R.348, E:K.426, E:K.426

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Laverty, D. et al., Cryo-EM structure of the human alpha 1 beta 3 gamma 2 GABAAreceptor in a lipid bilayer. Nature (2019)

Release Date

2019-01-02

Peptides

Gamma-aminobutyric acid receptor subunit beta-3: AC
Gamma-aminobutyric acid receptor subunit alpha-1: BE
Gamma-aminobutyric acid receptor subunit gamma-2: D
Megabody38: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

C
B

B
A

E
D

D
C

F
G

Membrane

We predict this structure to be a membrane protein.
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Gamma-aminobutyric acid receptor subunit beta-3

Gamma-aminobutyric acid receptor subunit alpha-1

Gamma-aminobutyric acid receptor subunit gamma-2

Megabody38

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