SMTL ID : 8jj1.1

Cryo-EM structure of GluN1-2A NMDAR in complex with human Fab2G7 in two fab conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-mer

Ligands

1 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: 3 residues within 4Å: Chain C: I.26, N.61, A.62 No protein-ligand interaction detected (PLIP)

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

NAG.2: 4 residues within 4Å: Chain B: K.487, P.686, N.687, K.711 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.487, B:N.687, B:K.711 NAG.3: 1 residues within 4Å: Chain C: N.276 No protein-ligand interaction detected (PLIP) NAG.4: 4 residues within 4Å: Chain C: N.368, G.369, I.373 Ligands: NAG.5 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.368, C:G.369 NAG.5: 4 residues within 4Å: Chain C: T.335, N.350, N.368 Ligands: NAG.4 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.350, C:N.368 NAG.6: 3 residues within 4Å: Chain C: P.767, W.768, N.771 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:P.767, C:W.768 Hydrogen bonds: C:N.771 NAG.7: 1 residues within 4Å: Chain D: N.687 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.687 NAG.8: 4 residues within 4Å: Chain E: I.26, N.61, A.62, T.63 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:I.26 Hydrogen bonds: E:N.61 NAG.9: 1 residues within 4Å: Chain E: N.276 No protein-ligand interaction detected (PLIP) NAG.10: 3 residues within 4Å: Chain E: N.368, G.369, H.371 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.368, E:H.371 NAG.11: 3 residues within 4Å: Chain E: G.336, R.337, N.350 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.350 NAG.12: 2 residues within 4Å: Chain E: M.470, N.771 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., Structural basis for antibody-mediated NMDA receptor clustering and endocytosis in autoimmune encephalitis. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-06-05

Peptides

Fab 2G7 Heavy Chain: AF
Glutamate receptor ionotropic, NMDA 2A: BD
Glutamate receptor ionotropic, NMDA 1: CE
Fab 2G7 Light Chain: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

F
E

B
A

D
C

C
B

E
D

G
F

H
G

Membrane

We predict this structure to be a membrane protein.
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Fab 2G7 Heavy Chain

Glutamate receptor ionotropic, NMDA 2A

Glutamate receptor ionotropic, NMDA 1

Fab 2G7 Light Chain

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