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- PDB-9c7p: Diheteromeric GluN1/GluN2A (delM653) in digitonin complexed with ... -

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Basic information

Entry
Database: PDB / ID: 9c7p
TitleDiheteromeric GluN1/GluN2A (delM653) in digitonin complexed with glycine, glutamate, and GNE-4123
Components
  • Glutamate receptor ionotropic, NMDA 1, Green fluorescent protein chimera
  • Glutamate receptor ionotropic, NMDA 2A, Green fluorescent protein chimera
KeywordsTRANSPORT PROTEIN / ion channel / NMDA / positive allosteric modulator / pre-open pore conformation
Function / homology
Function and homology information


neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / directional locomotion / pons maturation / response to environmental enrichment / positive regulation of Schwann cell migration / regulation of cell communication / EPHB-mediated forward signaling ...neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / 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 / cellular response to magnesium ion / transmitter-gated monoatomic ion channel activity / positive regulation of inhibitory postsynaptic potential / suckling behavior / response to methylmercury / response to glycine / propylene metabolic process / response to manganese ion / sleep / response to carbohydrate / locomotion / regulation of NMDA receptor activity / dendritic spine organization / cellular response to dsRNA / cellular response to lipid / 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 / response to lithium ion / positive regulation of calcium ion transport into cytosol / response to light stimulus / regulation of neuron apoptotic process / regulation of postsynaptic membrane potential / cellular response to glycine / associative learning / modulation of excitatory postsynaptic potential / action potential / monoatomic cation transport / excitatory synapse / conditioned place preference / 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 / cell adhesion molecule binding / cellular response to manganese ion / glutamate-gated calcium ion channel activity / presynaptic active zone membrane
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
Glutamate receptor ionotropic, NMDA 1 / Green fluorescent protein / Glutamate receptor ionotropic, NMDA 2A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Aequorea victoria (jellyfish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.61 Å
AuthorsJalali-Yazdi, F. / Kim, 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: Diheteromeric NMDA receptor GluN1/GluN2A, in complex with glycine, glutamate, and GNE-4123
Authors: Jalali-Yazdi, F. / Kim, J. / Gouaux, E.
History
DepositionJun 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 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

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, NMDA 1, Green fluorescent protein chimera
B: Glutamate receptor ionotropic, NMDA 2A, Green fluorescent protein chimera
C: Glutamate receptor ionotropic, NMDA 1, Green fluorescent protein chimera
D: Glutamate receptor ionotropic, NMDA 2A, Green fluorescent protein chimera


Theoretical massNumber of molelcules
Total (without water)502,2314
Polymers502,2314
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 124759.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Aequorea victoria (jellyfish)
Gene: Grin1, Nmdar1, GFP / Production host: Homo sapiens (human) / References: UniProt: P35439, UniProt: P42212
#2: Protein Glutamate receptor ionotropic, NMDA 2A, Green fluorescent protein chimera / 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: 126356.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Aequorea victoria (jellyfish)
Gene: Grin2a, GFP / Production host: Homo sapiens (human) / References: UniProt: Q00959, UniProt: P42212
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: Diheteromeric NMDA receptor GluN1/GluN2A, in complex with glycine, glutamate, and GNE-4123
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.502 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Rattus norvegicus (Norway rat)10116
31Aequorea victoria (jellyfish)6100
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 9
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K

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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: 2000 nm / Nominal defocus min: 800 nm
Image recordingAverage exposure time: 7.9 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of real images: 3916

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Processing

EM software
IDNameVersionCategory
2Leginonimage acquisition
7UCSF Chimera1.16model fitting
9PHENIX1.21model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 820000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 133000 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient

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