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- PDB-9pzr: GluN1/GluN2A in complex with polyclonal autoantibody Fab fragment... -

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Basic information

Entry
Database: PDB / ID: 9pzr
TitleGluN1/GluN2A in complex with polyclonal autoantibody Fab fragments (class 2), glycine- and glutamate-bound state
Components
  • Glutamate receptor ionotropic, NMDA 1
  • Glutamate receptor ionotropic, NMDA 2A
  • Polyclonal antibody Fab fragment, termed FabEnc1
KeywordsTRANSPORT PROTEIN / ligand-gated ion channel / NMDA / antibody / complex
Function / homology
Function and homology information


regulation of response to alcohol / response to ammonium ion / response to environmental enrichment / neurotransmitter receptor transport, plasma membrane to endosome / receptor recycling / directional locomotion / auditory behavior / pons maturation / EPHB-mediated forward signaling / positive regulation of Schwann cell migration ...regulation of response to alcohol / response to ammonium ion / response to environmental enrichment / neurotransmitter receptor transport, plasma membrane to endosome / receptor recycling / directional locomotion / auditory behavior / pons maturation / EPHB-mediated forward signaling / positive regulation of Schwann cell migration / Assembly and cell surface presentation of NMDA receptors / regulation of cell communication / response to carbohydrate / suckling behavior / cellular response to magnesium ion / olfactory learning / response to other organism / response to methylmercury / response to hydrogen sulfide / protein localization to postsynaptic membrane / dendritic branch / conditioned taste aversion / sleep / regulation of ARF protein signal transduction / transmitter-gated monoatomic ion channel activity / response to manganese ion / serotonin metabolic process / response to glycoside / cellular response to dsRNA / regulation of respiratory gaseous exchange / cellular response to lipid / propylene metabolic process / response to glycine / dendritic spine organization / locomotion / regulation of NMDA receptor activity / neuromuscular process / RAF/MAP kinase cascade / positive regulation of inhibitory postsynaptic potential / neurotransmitter receptor complex / response to amine / Synaptic adhesion-like molecules / NMDA glutamate receptor activity / regulation of monoatomic cation transmembrane transport / cellular response to zinc ion / NMDA selective glutamate receptor complex / glutamate binding / voltage-gated monoatomic cation channel activity / regulation of axonogenesis / ligand-gated sodium channel activity / response to morphine / calcium ion transmembrane import into cytosol / regulation of synapse assembly / male mating behavior / positive regulation of reactive oxygen species biosynthetic process / startle response / protein heterotetramerization / regulation of dendrite morphogenesis / spinal cord development / dopamine metabolic process / glycine binding / response to lithium ion / parallel fiber to Purkinje cell synapse / positive regulation of calcium ion transport into cytosol / glutamate receptor signaling pathway / social behavior / regulation of neuronal synaptic plasticity / associative learning / regulation of postsynaptic membrane potential / action potential / neuron development / cellular response to glycine / multicellular organismal response to stress / response to light stimulus / modulation of excitatory postsynaptic potential / positive regulation of dendritic spine maintenance / monoatomic cation transmembrane transport / positive regulation of protein targeting to membrane / Unblocking of NMDA receptors, glutamate binding and activation / monoatomic cation transport / glutamate receptor binding / ligand-gated monoatomic ion channel activity / prepulse inhibition / conditioned place preference / long-term memory / calcium ion homeostasis / phosphatase binding / adult locomotory behavior / postsynaptic density, intracellular component / neurogenesis / synaptic cleft / response to fungicide / monoatomic cation channel activity / cellular response to manganese ion / glutamate-gated receptor activity / positive regulation of synaptic transmission, glutamatergic / sensory perception of pain / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / cell adhesion molecule binding
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.92 Å
AuthorsKim, J. / Jalali-Yazdi, F. / Gouaux, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
CitationJournal: Sci Adv / Year: 2026
Title: Cryo-EM of autoantibody-bound NMDA receptors reveals antigenic hotspots in an active immunization model of anti-NMDAR encephalitis.
Authors: Junhoe Kim / Farzad Jalali-Yazdi / Brian E Jones / Gary L Westbrook / Eric Gouaux /
Abstract: Autoantibodies 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.
History
DepositionAug 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, NMDA 1
B: Glutamate receptor ionotropic, NMDA 2A
C: Glutamate receptor ionotropic, NMDA 1
D: Glutamate receptor ionotropic, NMDA 2A
E: Polyclonal antibody Fab fragment, termed FabEnc1
F: Polyclonal antibody Fab fragment, termed FabEnc1
G: Polyclonal antibody Fab fragment, termed FabEnc1
H: Polyclonal antibody Fab fragment, termed FabEnc1


Theoretical massNumber of molelcules
Total (without water)468,2058
Polymers468,2058
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Glutamate receptor ionotropic, NMDA 1 / GluN1 / Glutamate [NMDA] receptor subunit zeta-1 / N-methyl-D-aspartate receptor subunit NR1 / NMD-R1


Mass: 95372.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin1, Nmdar1 / Production host: Homo sapiens (human) / References: UniProt: P35439
#2: Protein Glutamate receptor ionotropic, NMDA 2A / GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / ...GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / NMDAR2A / NR2A


Mass: 97163.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2a / Production host: Homo sapiens (human) / References: UniProt: Q00959
#3: Antibody
Polyclonal antibody Fab fragment, termed FabEnc1


Mass: 20783.529 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: GluN1/GluN2A in complex with polyclonal autoantibody Fab fragments (class 2), glycine- and glutamate-bound state
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.602 MDa / Experimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 290 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1400 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 4119
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.0particle selection
9PHENIX1.20.model refinement
10cryoSPARC4.4.0initial Euler assignment
11cryoSPARC4.4.0final Euler assignment
13cryoSPARC4.4.03D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54790 / Symmetry type: POINT
RefinementHighest resolution: 3.92 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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