SMTL ID : 7t0w.1

Complex of GABA-A synaptic receptor with autoimmune antibody Fab115

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-2-2-mer

Ligands

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

NAG-NAG.1: 5 residues within 4Å: Chain A: P.78, L.79, N.80, H.119, R.169 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain C: P.78, L.79, N.80, H.119, P.120 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 9 residues within 4Å: Chain C: D.89 Chain D: N.88, N.111, T.113, M.114, P.115 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.7, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.7, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.7 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 7 residues within 4Å: Chain E: Q.219, W.220, K.221, R.222, L.243, R.244, N.245 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.222, E:R.222

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 8 residues within 4Å: Chain C: N.149, T.151, D.190, K.192, I.194, K.196, S.211, K.213 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.196 NAG-NAG-BMA.6: 8 residues within 4Å: Chain A: N.149, D.190, Y.191, K.192, I.194, K.196, S.211, K.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.192, A:K.196

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN-MAN-MAN-MAN.7: 27 residues within 4Å: Chain A: V.106, G.108, V.109, K.112 Chain B: N.111, M.112, T.113 Chain D: N.28, N.88, A.109, N.111, P.115, K.117 Chain E: S.137, N.138, V.140, G.141, K.142, K.155, A.156, D.157, A.158, W.160, T.163, P.164, R.166 Ligands: NAG-NAG.4 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Noviello, C.M. et al., Structural mechanisms of GABA A receptor autoimmune encephalitis. Cell (2022)

Release Date

2022-07-13

Peptides

Gamma-aminobutyric acid receptor subunit beta-2: AC
Gamma-aminobutyric acid receptor subunit alpha-1: BD
Gamma-aminobutyric acid receptor subunit gamma-2: E
Fab115 light chain, IgG1: FI
Fab115 Heavy Chain, IgG1: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
L2

I
L

G
H

H
H2

Membrane

We predict this structure to be a membrane protein.
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Gamma-aminobutyric acid receptor subunit beta-2

Gamma-aminobutyric acid receptor subunit alpha-1

Gamma-aminobutyric acid receptor subunit gamma-2

Fab115 light chain, IgG1

Fab115 Heavy Chain, IgG1

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