SMTL ID : 8jiz.1

Cryo-EM structure of GluN1-2A NMDAR in complex with human Fab5F6 in two fab bind conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-mer

Ligands

5 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: 4 residues within 4Å: Chain B: N.61, A.62, T.63, S.85 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 9 residues within 4Å: Chain B: M.41, N.273, N.276, S.278, A.279 Chain E: Y.52, S.73, T.75, K.76 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.76 NAG-NAG.3: 2 residues within 4Å: Chain B: W.768, N.771 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain D: N.61, A.62, T.63 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 9 residues within 4Å: Chain D: M.41, N.276, S.278, A.279, S.282, V.334 Chain G: Y.52, T.75, K.76 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain G Hydrogen bonds: D:S.278, G:T.75, G:T.75

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

NAG.6: 3 residues within 4Å: Chain A: V.489, N.687, K.711 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.489 NAG.7: 1 residues within 4Å: Chain B: N.471 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.471 NAG.8: 2 residues within 4Å: Chain B: N.203, T.205 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.203 NAG.9: 3 residues within 4Å: Chain C: K.484, N.687, K.711 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.687 NAG.10: 4 residues within 4Å: Chain D: F.348, N.368, G.369, H.371 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.368 NAG.11: 1 residues within 4Å: Chain D: N.471 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.471 NAG.12: 3 residues within 4Å: Chain D: M.470, W.768, N.771 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.768 NAG.13: 2 residues within 4Å: Chain D: N.203, T.205 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.203, D:T.205

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

Glutamate receptor ionotropic, NMDA 2A: AC
Glutamate receptor ionotropic, NMDA 1: BD
Fab5F6 Heavy Chain: EG
Fab5F6 Light Chain: FH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

G
G

F
F

H
H

Membrane

We predict this structure to be a membrane protein.
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Glutamate receptor ionotropic, NMDA 2A

Glutamate receptor ionotropic, NMDA 1

Fab5F6 Heavy Chain

Fab5F6 Light Chain

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