SMTL ID : 7t0z.1

Complex of GABA-A synaptic receptor with autoimmune antibody Fab175

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.1: 4 residues within 4Å: Chain A: P.78, L.79, N.80, H.119 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain C: P.78, L.79, N.80, H.119 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain E: Q.219, W.220, R.222, V.225, L.243, R.244, N.245 No protein-ligand interaction detected (PLIP)

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: 10 residues within 4Å: Chain C: N.149, T.151, D.190, Y.191, K.192, I.194, K.196, S.211, F.212, K.213 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 9 residues within 4Å: Chain A: N.149, D.190, Y.191, K.192, I.194, K.196, S.211, F.212, 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: 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-(1-6)]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.6: 27 residues within 4Å: Chain A: R.86, V.106, K.112 Chain B: N.111, M.112, T.113, P.115 Chain D: N.28, N.88, S.92, K.93, A.109, N.111, P.115, K.117 Chain E: S.137, N.138, M.139, V.140, G.141, K.142, D.157, W.160, P.164, R.166 Ligands: NAG.10, MAN.11 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.88, D:N.88, D:A.109, D:K.117

2 x ABU: GAMMA-AMINO-BUTANOIC ACID(Non-covalent)

ABU.7: 8 residues within 4Å: Chain A: Y.97, Y.157, S.201, T.202, Y.205 Chain B: F.65, R.67, T.130 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.97, A:Y.157, B:T.130 Hydrophobic interactions: B:F.65, B:T.130 Salt bridges: B:R.67 ABU.8: 8 residues within 4Å: Chain C: Y.97, Y.157, F.200, T.202, Y.205 Chain D: F.65, R.67, T.130 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.65, D:T.130, C:T.202 Hydrogen bonds: D:T.130, D:T.130, C:Y.157 Salt bridges: D:R.67

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

NAG.9: 3 residues within 4Å: Chain C: D.89 Chain D: M.114 Ligands: NAG.10 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.89 NAG.10: 8 residues within 4Å: Chain D: N.111, T.113, M.114, P.115 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.6, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.6, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.6, NAG.9 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.111

1 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.11: 7 residues within 4Å: Chain A: G.108, V.109, K.112 Chain E: A.156, D.157 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.6, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.6 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.157

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
Fab175 IgG1 heavy chain: F
Fab175 IgG1 light chain: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
H

G
L

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

Fab175 IgG1 heavy chain

Fab175 IgG1 light chain

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