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- PDB-9pzt: Native GluN1/GluN2A in complex with 5F11 and 3D2 Fabs (class 3), ... -

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Basic information

Entry
Database: PDB / ID: 9pzt
TitleNative GluN1/GluN2A in complex with 5F11 and 3D2 Fabs (class 3), glycine and glutamate-bound state
Components
  • (Glutamate receptor ionotropic, NMDA ...) x 2
  • (Heavy chain of ...) x 2
  • (Light chain of ...) x 2
KeywordsTRANSPORT PROTEIN / ligand-gated ion channel / NMDA / antibody / native
Function / homology
Function and homology information


Assembly and cell surface presentation of NMDA receptors / EPHB-mediated forward signaling / Synaptic adhesion-like molecules / Unblocking of NMDA receptors, glutamate binding and activation / neurotransmitter receptor transport, plasma membrane to endosome / RAF/MAP kinase cascade / receptor recycling / directional locomotion / pons maturation / positive regulation of Schwann cell migration ...Assembly and cell surface presentation of NMDA receptors / EPHB-mediated forward signaling / Synaptic adhesion-like molecules / Unblocking of NMDA receptors, glutamate binding and activation / neurotransmitter receptor transport, plasma membrane to endosome / RAF/MAP kinase cascade / receptor recycling / directional locomotion / pons maturation / positive regulation of Schwann cell migration / regulation of cell communication / olfactory learning / serotonin metabolic process / dendritic branch / conditioned taste aversion / protein localization to postsynaptic membrane / regulation of ARF protein signal transduction / suckling behavior / transmitter-gated monoatomic ion channel activity / sleep / regulation of respiratory gaseous exchange / propylene metabolic process / response to glycine / dendritic spine organization / locomotion / regulation of NMDA receptor activity / positive regulation of inhibitory postsynaptic potential / neurotransmitter receptor complex / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / glutamate binding / voltage-gated monoatomic cation channel activity / neuromuscular process / ligand-gated sodium channel activity / glutamate receptor signaling pathway / transport vesicle membrane / regulation of axonogenesis / calcium ion transmembrane import into cytosol / monoatomic ion channel complex / response to morphine / male mating behavior / regulation of dendrite morphogenesis / protein heterotetramerization / positive regulation of reactive oxygen species biosynthetic process / regulation of synapse assembly / glycine binding / dopamine metabolic process / startle response / cellular response to zinc ion / response to lithium ion / parallel fiber to Purkinje cell synapse / regulation of neuronal synaptic plasticity / regulation of postsynaptic membrane potential / associative learning / positive regulation of calcium ion transport into cytosol / modulation of excitatory postsynaptic potential / positive regulation of dendritic spine maintenance / action potential / monoatomic cation transmembrane transport / positive regulation of protein targeting to membrane / monoatomic cation transport / glutamate receptor binding / social behavior / ligand-gated monoatomic ion channel activity / prepulse inhibition / phosphatase binding / long-term memory / postsynaptic density, intracellular component / calcium ion homeostasis / synaptic cleft / monoatomic cation channel activity / adult locomotory behavior / glutamate-gated receptor activity / positive regulation of synaptic transmission, glutamatergic / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / neurogenesis / cell adhesion molecule binding / ionotropic glutamate receptor signaling pathway / excitatory synapse / ionotropic glutamate receptor binding / sensory perception of pain / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoplasmic vesicle membrane / regulation of neuron apoptotic process / protein tyrosine kinase binding / response to amphetamine / excitatory postsynaptic potential / positive regulation of excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / learning / sodium ion transmembrane transport / synaptic membrane / cellular response to amino acid stimulus / regulation of long-term neuronal synaptic plasticity / synaptic transmission, glutamatergic / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential
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 2A / Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.14 Å
AuthorsKim, J. / 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
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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
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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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Heavy chain of GluN2A-specific monoclonal Fab fragment, termed 3D2
M: Light chain of GluN2A-specific monoclonal Fab fragment, termed 3D2
D: Glutamate receptor ionotropic, NMDA 2A
C: Glutamate receptor ionotropic, NMDA 1
H: Heavy chain of GluN1-specific monoclonal Fab fragment, termed 5F11
I: Light chain of GluN1-specific monoclonal Fab fragment, termed 5F11
J: Heavy chain of GluN2A-specific monoclonal Fab fragment, termed 3D2
K: Light chain of GluN2A-specific monoclonal Fab fragment, termed 3D2
B: Glutamate receptor ionotropic, NMDA 2A
A: Glutamate receptor ionotropic, NMDA 1
F: Heavy chain of GluN1-specific monoclonal Fab fragment, termed 5F11
G: Light chain of GluN1-specific monoclonal Fab fragment, termed 5F11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)714,46213
Polymers714,03712
Non-polymers4241
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

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Glutamate receptor ionotropic, NMDA ... , 2 types, 4 molecules DBCA

#3: 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: 165619.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P35436
#4: Protein Glutamate receptor ionotropic, NMDA 1 / GluN1 / Glutamate [NMDA] receptor subunit zeta-1 / N-methyl-D-aspartate receptor subunit NR1 / NMD-R1


Mass: 105617.820 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P35438

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Antibody , 4 types, 8 molecules LJMKHFIG

#1: Antibody Heavy chain of GluN2A-specific monoclonal Fab fragment, termed 3D2


Mass: 15448.522 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)
#2: Antibody Light chain of GluN2A-specific monoclonal Fab fragment, termed 3D2


Mass: 13989.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)
#5: Antibody Heavy chain of GluN1-specific monoclonal Fab fragment, termed 5F11


Mass: 29432.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)
#6: Antibody Light chain of GluN1-specific monoclonal Fab fragment, termed 5F11


Mass: 26909.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)

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Sugars , 1 types, 1 molecules

#7: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Details

Has ligand of interestY
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: Native GluN1/GluN2A in complex with 5F11 and 3D2 Fabs (class 3), glycine and glutamate-bound state
Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Molecular weightValue: 0.717 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 0.05 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: 3000 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 65 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 9851
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: 6.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26341 / Symmetry type: POINT
RefinementHighest resolution: 6.14 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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