SMTL ID : 6hug.1

CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with picrotoxin and megabody Mb38.

Coordinates

PDB Format Compare

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: 13 residues within 4Å: Chain A: N.119, T.121 Chain C: S.139, N.140, V.142, G.143, K.144, D.159, W.162, P.166 Chain D: N.36, S.100 Ligands: NAG-NAG-BMA-MAN-MAN.5 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:D.159, D:K.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 B: P.103, N.105, H.144 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain C: W.222, S.226, L.245, N.247 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain E: P.103, L.104, 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: 7 residues within 4Å: Chain B: N.174, R.217, V.219, S.220, R.221, S.236, R.238 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.217, B:R.221 NAG-NAG-BMA-MAN-MAN-MAN.7: 7 residues within 4Å: Chain E: N.174, E.215, R.217, V.219, S.220, R.221, S.236 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.5: 6 residues within 4Å: Chain A: L.97 Chain D: N.119, P.123 Chain E: D.114 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.1 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.114, E:D.114

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.8: 12 residues within 4Å: Chain A: R.257, T.314, F.318, T.319, K.320, R.321, N.395, S.396, S.398, K.399, I.400, L.403 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:T.314, A:I.400, A:L.403 Hydrogen bonds: A:R.257, A:R.257, A:F.318, A:S.396, A:S.396, A:K.399 Salt bridges: A:R.257, A:K.320, A:R.321 PIO.10: 11 residues within 4Å: Chain D: R.257, T.314, F.318, K.320, R.321, N.395, S.396, S.398, K.399, I.400, L.403 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:T.314, D:I.400, D:L.403 Hydrogen bonds: D:R.257, D:F.318, D:S.396, D:S.396, D:K.399 Salt bridges: D:R.257, D:K.320, D:K.320, D:R.321

1 x RI5: (1aR,2aR,3S,6R,6aS,8aS,8bR,9R)-2a-hydroxy-8b-methyl-9-(prop-1-en-2-yl)hexahydro-3,6-methano-1,5,7-trioxacyclopenta[ij]c yclopropa[a]azulene-4,8(3H)-dione(Non-covalent)

RI5.9: 14 residues within 4Å: Chain A: V.265, T.269 Chain B: A.277, I.280, T.281 Chain C: S.306, T.310, L.313 Chain D: V.265, T.269, L.272 Chain E: A.277, T.281, L.284 6 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: C:L.313, D:V.265, D:T.269, D:L.272, E:T.281, E:L.284

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Masiulis, S. et al., GABAAreceptor signalling mechanisms revealed by structural pharmacology. Nature (2019)

Release Date

2019-01-02

Peptides

Gamma-aminobutyric acid receptor subunit alpha-1: AD
Gamma-aminobutyric acid receptor subunit beta-3: BE
Gamma-aminobutyric acid 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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Gamma-aminobutyric acid receptor subunit alpha-1

Gamma-aminobutyric acid receptor subunit beta-3

Gamma-aminobutyric acid receptor subunit gamma-2

Megabody Mb38

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