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- PDB-9pzv: Native GluN1/GluN2A in complex with 5F11 and 3D2 Fabs, local ATD dimer -

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Basic information

Entry
Database: PDB / ID: 9pzv
TitleNative GluN1/GluN2A in complex with 5F11 and 3D2 Fabs, local ATD dimer
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 / Synaptic adhesion-like molecules / EPHB-mediated forward signaling / Unblocking of NMDA receptors, glutamate binding and activation / RAF/MAP kinase cascade / directional locomotion / pons maturation / regulation of cell communication / olfactory learning / conditioned taste aversion ...Assembly and cell surface presentation of NMDA receptors / Synaptic adhesion-like molecules / EPHB-mediated forward signaling / Unblocking of NMDA receptors, glutamate binding and activation / RAF/MAP kinase cascade / directional locomotion / pons maturation / regulation of cell communication / olfactory learning / conditioned taste aversion / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane / serotonin metabolic process / suckling behavior / propylene metabolic process / sleep / locomotion / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / neurotransmitter receptor complex / ligand-gated sodium channel activity / response to morphine / glutamate receptor signaling pathway / regulation of axonogenesis / neuromuscular process / calcium ion transmembrane import into cytosol / regulation of dendrite morphogenesis / transport vesicle membrane / protein heterotetramerization / male mating behavior / regulation of synapse assembly / glycine binding / startle response / dopamine metabolic process / monoatomic cation transmembrane transport / regulation of postsynaptic membrane potential / associative learning / social behavior / regulation of neuronal synaptic plasticity / monoatomic cation transport / positive regulation of excitatory postsynaptic potential / long-term memory / prepulse inhibition / positive regulation of synaptic transmission, glutamatergic / monoatomic cation channel activity / calcium ion homeostasis / regulation of neuron apoptotic process / glutamate-gated calcium ion channel activity / neurogenesis / sensory perception of pain / ionotropic glutamate receptor signaling pathway / sodium ion transmembrane transport / synaptic membrane / cytoplasmic vesicle membrane / response to amphetamine / adult locomotory behavior / learning / regulation of membrane potential / synaptic transmission, glutamatergic / excitatory postsynaptic potential / locomotory behavior / protein catabolic process / regulation of long-term neuronal synaptic plasticity / neuron cellular homeostasis / postsynaptic density membrane / cerebral cortex development / regulation of synaptic plasticity / negative regulation of protein catabolic process / visual learning / modulation of chemical synaptic transmission / calcium ion transmembrane transport / response to wounding / calcium channel activity / memory / long-term synaptic potentiation / intracellular calcium ion homeostasis / synaptic vesicle / synaptic vesicle membrane / calcium ion transport / growth cone / presynaptic membrane / response to ethanol / dendritic spine / chemical synaptic transmission / negative regulation of neuron apoptotic process / postsynaptic membrane / transcription by RNA polymerase II / learning or memory / calmodulin binding / neuron projection / postsynapse / postsynaptic density / positive regulation of apoptotic process / response to xenobiotic stimulus / signaling receptor binding / calcium ion binding / synapse / dendrite / endoplasmic reticulum membrane
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 / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : ...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 / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / 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: 3.92 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: To Be Published
Title: Native GluN1/GluN2A in complex with 5F11 and 3D2 Fabs, local ATD dimer
Authors: Kim, J. / Gouaux, E.
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

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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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,43416
Polymers357,0196
Non-polymers2,41510
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, 2 molecules AB

#1: 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.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P35438
#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: 165619.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P35436

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Antibody , 4 types, 4 molecules HIJK

#3: Antibody Heavy chain of GluN1-specific monoclonal Fab fragment, termed 5F11


Mass: 29432.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)
#4: Antibody Light chain of GluN1-specific monoclonal Fab fragment, termed 5F11


Mass: 26909.961 Da / Num. of mol.: 1
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 GluN2A-specific monoclonal Fab fragment, termed 3D2


Mass: 15448.522 Da / Num. of mol.: 1
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 GluN2A-specific monoclonal Fab fragment, termed 3D2


Mass: 13989.831 Da / Num. of mol.: 1
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 , 2 types, 10 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
#8: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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, local ATD dimer
Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Molecular weightValue: 0.23 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: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 624529 / Symmetry type: POINT
RefinementHighest resolution: 3.92 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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