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- PDB-8jf7: Triheteromeric NMDA receptor GluN1-GluN2A-GluN3A in complex with ... -

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Basic information

Entry
Database: PDB / ID: 8jf7
TitleTriheteromeric NMDA receptor GluN1-GluN2A-GluN3A in complex with glycine, glutamate, a GluN1-specific Fab,and a GluN2A-specific Fab
Components
  • (GluN1-specific antibody fragment ...) x 2
  • (GluN2A-specific antibody fragment ...) x 2
  • (Glutamate receptor ionotropic, NMDA ...) x 3
KeywordsMEMBRANE PROTEIN / ion channel
Function / homology
Function and homology information


serine binding / neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / negative regulation of dendritic spine development / receptor recycling / directional locomotion / pons maturation / response to environmental enrichment / positive regulation of Schwann cell migration ...serine binding / neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / negative regulation of dendritic spine development / receptor recycling / directional locomotion / pons maturation / response to environmental enrichment / positive regulation of Schwann cell migration / regulation of cell communication / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / auditory behavior / olfactory learning / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / serotonin metabolic process / response to other organism / protein localization to postsynaptic membrane / regulation of ARF protein signal transduction / transmitter-gated monoatomic ion channel activity / cellular response to magnesium ion / positive regulation of inhibitory postsynaptic potential / suckling behavior / response to methylmercury / response to glycine / propylene metabolic process / response to manganese ion / response to carbohydrate / sleep / regulation of NMDA receptor activity / locomotion / dendritic spine organization / cellular response to dsRNA / cellular response to lipid / glutamate receptor activity / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / voltage-gated monoatomic cation channel activity / response to glycoside / NMDA selective glutamate receptor complex / glutamate binding / ligand-gated sodium channel activity / neurotransmitter receptor complex / glutamate receptor signaling pathway / response to morphine / calcium ion transmembrane import into cytosol / regulation of axonogenesis / neuromuscular process / regulation of dendrite morphogenesis / protein heterotetramerization / male mating behavior / glycine binding / regulation of synapse assembly / spinal cord development / response to amine / parallel fiber to Purkinje cell synapse / cellular response to zinc ion / startle response / positive regulation of reactive oxygen species biosynthetic process / monoatomic cation transmembrane transport / dopamine metabolic process / dendrite development / response to lithium ion / response to light stimulus / positive regulation of calcium ion transport into cytosol / regulation of postsynaptic membrane potential / cellular response to glycine / associative learning / modulation of excitatory postsynaptic potential / action potential / excitatory synapse / conditioned place preference / monoatomic cation transport / positive regulation of dendritic spine maintenance / social behavior / regulation of neuronal synaptic plasticity / monoatomic ion channel complex / positive regulation of protein targeting to membrane / glutamate receptor binding / positive regulation of excitatory postsynaptic potential / Unblocking of NMDA receptors, glutamate binding and activation / long-term memory / synaptic cleft / neuron development / positive regulation of synaptic transmission, glutamatergic / prepulse inhibition / phosphatase binding / multicellular organismal response to stress / postsynaptic density, intracellular component / monoatomic cation channel activity / calcium ion homeostasis / response to fungicide / glutamate-gated receptor activity / regulation of neuron apoptotic process
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Green fluorescent protein, GFP / 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 / : / : / Green fluorescent protein, GFP / 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 / : / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / 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
Enhanced green fluorescent protein / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2A / Glutamate receptor ionotropic, NMDA 3A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Muromegalovirus G4
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.73 Å
AuthorsKou, Z. / Zhu, S.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: Probing the architecture of native GluN1-N2-N3A NMDA receptors by cryo-EM and click chemistry.
Authors: Kou, Z. / Zhu, S.
History
DepositionMay 17, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.0May 22, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 22, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 22, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 22, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 22, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 22, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0May 22, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 22, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 22, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 22, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 22, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update
Revision 1.2Jul 23, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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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,Enhanced green fluorescent protein
C: Glutamate receptor ionotropic, NMDA 1
D: Glutamate receptor ionotropic, NMDA 3A,Enhanced green fluorescent protein
E: GluN1-specific antibody fragment light chain
F: GluN1-specific antibody fragment heavy chain
G: GluN1-specific antibody fragment light chain
H: GluN1-specific antibody fragment heavy chain
K: GluN2A-specific antibody fragment light chain
J: GluN2A-specific antibody fragment heavy chain


Theoretical massNumber of molelcules
Total (without water)599,94810
Polymers599,94810
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Glutamate receptor ionotropic, NMDA ... , 3 types, 4 molecules ACBD

#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,Enhanced green fluorescent protein / 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: 125325.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Muromegalovirus G4
Gene: Grin2a, eGFP / Production host: Homo sapiens (human) / References: UniProt: Q00959, UniProt: A0A7G8ZY66
#3: Protein Glutamate receptor ionotropic, NMDA 3A,Enhanced green fluorescent protein / GluN3A / Glutamate receptor chi-1 / N-methyl-D-aspartate receptor / N-methyl-D-aspartate receptor ...GluN3A / Glutamate receptor chi-1 / N-methyl-D-aspartate receptor / N-methyl-D-aspartate receptor subtype 3A / NMDAR3A / NR3A / NMDAR-L / NMDAR-L1


Mass: 137362.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Muromegalovirus G4
Gene: Grin3a, eGFP / Production host: Homo sapiens (human) / References: UniProt: Q9R1M7, UniProt: A0A7G8ZY66

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Antibody , 4 types, 6 molecules EGFHKJ

#4: Antibody GluN1-specific antibody fragment light chain


Mass: 25739.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#5: Antibody GluN1-specific antibody fragment heavy chain


Mass: 23432.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#6: Antibody GluN2A-specific antibody fragment light chain


Mass: 23234.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#7: Antibody GluN2A-specific antibody fragment heavy chain


Mass: 24936.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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Details

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: Triheteromeric NMDA receptor GluN1-GluN2A-GluN3A in complex with glycine, glutamate, a GluN1-specific Fab,and a GluN2A-specific Fab
Type: COMPLEX / Entity ID: #4-#5, #1-#3, #7, #6 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN 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: 1500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 162395 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00230527
ELECTRON MICROSCOPYf_angle_d0.38541503
ELECTRON MICROSCOPYf_dihedral_angle_d7.17218267
ELECTRON MICROSCOPYf_chiral_restr0.0374703
ELECTRON MICROSCOPYf_plane_restr0.0035389

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