9PZU | pdb_00009pzu

Native GluN1/GluN2B in complex with 5F11 Fab (class 4), glycine and glutamate-bound state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM of autoantibody-bound NMDA receptors reveals antigenic hotspots in an active immunization model of anti-NMDAR encephalitis.

Kim, J.Jalali-Yazdi, F.Jones, B.E.Westbrook, G.L.Gouaux, E.

(2026) Sci Adv 12: eaeb4249-eaeb4249

  • DOI: https://doi.org/10.1126/sciadv.aeb4249
  • Primary Citation of Related Structures:  
    9PZQ, 9PZR, 9PZS, 9PZT, 9PZU, 9PZV, 9PZW, 9PZX

  • PubMed Abstract: 

    Autoantibodies targeting synaptic membrane proteins are associated with autoimmune encephalitis manifested by seizures, psychosis, and memory dysfunction. Anti- N -methyl-d-aspartate receptor (NMDAR) encephalitis, a prototype of these autoimmune synaptic disorders, is unexpectedly common. Unfortunately, how the native repertoire of anti-NMDAR autoantibodies recognizes NMDARs and the precise locations of antigenic epitopes remain poorly understood. Here, we used an active immunization model that closely mimics the human disease to immunize adult mice with intact GluN1/GluN2A receptors, resulting in fulminant autoimmune encephalitis. Serum was collected at 6 weeks postimmunization for single-particle cryo-electron microscopy of GluN1/GluN2A receptors complexed with purified polyclonal anti-NMDAR autoantibody fragments. Native autoantibodies recognized two distinct binding sites on the GluN1 amino-terminal domain, which we confirmed using monoclonal antibodies bound to native NMDARs purified from mouse brain. Structural analysis of autoantibody-bound NMDAR complexes identified antigenic hotspots within the GluN1 amino-terminal domain. These hotspots provide potential targets for therapeutic intervention.


  • Organizational Affiliation
    • Vollum Institute, Oregon Health & Science University, 3232 SW Research Drive, Portland, OR 97239, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of GluN1-specific monoclonal Fab fragment, termed 5F11A [auth F],
D [auth H]
277Mus musculusMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of GluN1-specific monoclonal Fab fragment, termed 5F11B [auth G],
E [auth I]
244Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 1C [auth A],
F [auth C]
938Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P35438 (Mus musculus)
Explore P35438 
Go to UniProtKB:  P35438
IMPC:  MGI:95819
Entity Groups  
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UniProt GroupP35438
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P35438-1
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 2BG [auth D],
H [auth B]
1,482Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q01097 (Mus musculus)
Explore Q01097 
Go to UniProtKB:  Q01097
IMPC:  MGI:95821
Entity Groups  
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UniProt GroupQ01097
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q01097-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI [auth E],
J,
K,
L
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.
RECONSTRUCTIONcryoSPARC4.4.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release
  • Version 1.1: 2026-02-04
    Changes: Data collection, Database references