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- PDB-9ofi: GluN1/GluN3A in complex with CGP and DCKA, LBD-focused, in antago... -

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Basic information

Entry
Database: PDB / ID: 9ofi
TitleGluN1/GluN3A in complex with CGP and DCKA, LBD-focused, in antagonist-bound conformation
Components
  • Glutamate receptor ionotropic, NMDA 3A
  • Isoform E of Glutamate receptor ionotropic, NMDA 1
KeywordsTRANSPORT PROTEIN / ligand-gated ion channel / NMDA / inhibitor
Function / homology
Function and homology information


negative regulation of dendritic spine development / serine binding / mesencephalic trigeminal nucleus development / trigeminal motor nucleus development / pons maturation / EPHB-mediated forward signaling / positive regulation of Schwann cell migration / Assembly and cell surface presentation of NMDA receptors / regulation of cell communication / protein localization to postsynaptic membrane ...negative regulation of dendritic spine development / serine binding / mesencephalic trigeminal nucleus development / trigeminal motor nucleus development / pons maturation / EPHB-mediated forward signaling / positive regulation of Schwann cell migration / Assembly and cell surface presentation of NMDA receptors / regulation of cell communication / protein localization to postsynaptic membrane / conditioned taste aversion / suckling behavior / olfactory learning / dendritic branch / positive regulation of mitochondrial calcium ion concentration / response to glycoside / transmitter-gated monoatomic ion channel activity / regulation of respiratory gaseous exchange / propylene metabolic process / response to glycine / neurotransmitter receptor complex / RAF/MAP kinase cascade / response to amine / Synaptic adhesion-like molecules / negative regulation of dendritic spine maintenance / glutamate receptor activity / NMDA glutamate receptor activity / regulation of monoatomic cation transmembrane transport / neuromuscular process / NMDA selective glutamate receptor complex / glutamate binding / regulation of axonogenesis / ligand-gated sodium channel activity / startle response / voltage-gated monoatomic cation channel activity / regulation of synapse assembly / calcium ion transmembrane import into cytosol / response to morphine / positive regulation of reactive oxygen species biosynthetic process / male mating behavior / protein heterotetramerization / regulation of dendrite morphogenesis / dendrite development / glycine binding / parallel fiber to Purkinje cell synapse / positive regulation of calcium ion transport into cytosol / associative learning / hypothalamus development / regulation of neuronal synaptic plasticity / social behavior / monoatomic cation transmembrane transport / positive regulation of dendritic spine maintenance / cellular response to glycine / Unblocking of NMDA receptors, glutamate binding and activation / response to fungicide / monoatomic cation transport / calcium ion homeostasis / glutamate receptor binding / prepulse inhibition / phosphatase binding / long-term memory / adult locomotory behavior / regulation of long-term neuronal synaptic plasticity / monoatomic cation channel activity / response to amphetamine / glutamate-gated receptor activity / sensory perception of pain / cellular response to manganese ion / positive regulation of synaptic transmission, glutamatergic / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / visual learning / hippocampus development / synaptic cleft / presynaptic modulation of chemical synaptic transmission / regulation of neuron apoptotic process / ionotropic glutamate receptor signaling pathway / excitatory synapse / protein phosphatase 2A binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / learning / dendrite membrane / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / positive regulation of excitatory postsynaptic potential / brain development / sodium ion transmembrane transport / synaptic membrane / synaptic transmission, glutamatergic / cerebral cortex development / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / memory / response to calcium ion / regulation of synaptic plasticity / postsynaptic density membrane / modulation of chemical synaptic transmission / intracellular calcium ion homeostasis / calcium channel activity / calcium ion transmembrane transport
Similarity search - Function
: / : / 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. ...: / : / 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
Chem-J86 / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 3A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.41 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: GluN1/GluN3A in complex with CGP and DCKA, LBD-focused, in antagonist-bound conformation
Authors: Kim, J. / Gouaux, E.
History
DepositionApr 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform E of Glutamate receptor ionotropic, NMDA 1
C: Isoform E of Glutamate receptor ionotropic, NMDA 1
B: Glutamate receptor ionotropic, NMDA 3A
D: Glutamate receptor ionotropic, NMDA 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)415,24114
Polymers412,3094
Non-polymers2,93210
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 Isoform E of Glutamate receptor ionotropic, NMDA 1 / GluN1 / Glutamate [NMDA] receptor subunit zeta-1 / N-methyl-D-aspartate receptor subunit NR1 / NMD-R1


Mass: 97873.969 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 3A / 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: 108280.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin3a / Production host: Homo sapiens (human) / References: UniProt: Q9R1M7
#3: 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: 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.: 6 / 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
#5: Chemical ChemComp-J86 / [(1S)-1-[[7-bromanyl-2,3-bis(oxidanylidene)-1,4-dihydroquinoxalin-5-yl]methylamino]ethyl]phosphonic acid


Mass: 378.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H13BrN3O5P
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: di-heteromeric GluN1/GluN3A in complex with CGP and DCKA, LBD-focused, in antagonist-bound conformation
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen 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: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1-4487 / Category: model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80690 / Symmetry type: POINT
RefinementHighest resolution: 3.41 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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