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TitleCryo-EM of autoantibody-bound NMDA receptors reveals antigenic hotspots in an active immunization model of anti-NMDAR encephalitis.
Journal, issue, pagesSci Adv, Vol. 12, Issue 3, Page eaeb4249, Year 2026
Publish dateJan 16, 2026
AuthorsJunhoe Kim / Farzad Jalali-Yazdi / Brian E Jones / Gary L Westbrook / Eric Gouaux /
PubMed AbstractAutoantibodies targeting synaptic membrane proteins are associated with autoimmune encephalitis manifested by seizures, psychosis, and memory dysfunction. Anti--methyl-d-aspartate receptor (NMDAR) ...Autoantibodies targeting synaptic membrane proteins are associated with autoimmune encephalitis manifested by seizures, psychosis, and memory dysfunction. Anti--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.
External linksSci Adv / PubMed:41533802 / PubMed Central
MethodsEM (single particle)
Resolution2.76 - 6.56 Å
Structure data

72076

9pzq

EMDB-72076, PDB-9pzq:
GluN1/GluN2A in complex with polyclonal autoantibody Fab fragments (class 1), glycine- and glutamate-bound state
Method: EM (single particle) / Resolution: 4.07 Å

72077

9pzr

EMDB-72077, PDB-9pzr:
GluN1/GluN2A in complex with polyclonal autoantibody Fab fragments (class 2), glycine- and glutamate-bound state
Method: EM (single particle) / Resolution: 3.92 Å

72078

9pzs

EMDB-72078, PDB-9pzs:
Native GluN1/GluN2A/GluN2B in complex with 5F11 and 3D2 Fabs (class 1), glycine and glutamate bound state
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-72079: Native GluN1/GluN2A/GluNx in complex with 5F11 and 3D2 Fabs (class 2), glycine and glutamate-bound state
Method: EM (single particle) / Resolution: 6.56 Å

72080

9pzt

EMDB-72080, PDB-9pzt:
Native GluN1/GluN2A in complex with 5F11 and 3D2 Fabs (class 3), glycine and glutamate-bound state
Method: EM (single particle) / Resolution: 6.14 Å

72081

9pzu

EMDB-72081, PDB-9pzu:
Native GluN1/GluN2B in complex with 5F11 Fab (class 4), glycine and glutamate-bound state
Method: EM (single particle) / Resolution: 5.36 Å

EMDB-72082: Native GluN1/GluNx in complex with 5F11 Fab (class 5), glycine and glutamate-bound state
Method: EM (single particle) / Resolution: 5.05 Å

72083

9pzv

EMDB-72083, PDB-9pzv:
Native GluN1/GluN2A in complex with 5F11 and 3D2 Fabs, local ATD dimer
Method: EM (single particle) / Resolution: 3.92 Å

72084

9pzw

EMDB-72084, PDB-9pzw:
GluN1/GluN2A in complex with 3D2 Fab, glycine and glutamate-bound state
Method: EM (single particle) / Resolution: 3.43 Å

72085

9pzx

EMDB-72085, PDB-9pzx:
GluN1/GluN2A in complex with 3D2 Fab, local ATD dimer
Method: EM (single particle) / Resolution: 2.76 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-GLY:
GLYCINE

ChemComp-GLU:
GLUTAMIC ACID

Source
  • rattus norvegicus (Norway rat)
  • mus musculus (house mouse)
KeywordsTRANSPORT PROTEIN / ligand-gated ion channel / NMDA / antibody / complex / native

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