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- PDB-9oou: Glycine/Glutamate/EU 1622-240 rGluN1a-2B NMDAR -

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Basic information

Entry
Database: PDB / ID: 9oou
TitleGlycine/Glutamate/EU 1622-240 rGluN1a-2B NMDAR
Components(Glutamate receptor ionotropic, NMDA ...) x 2
KeywordsMEMBRANE PROTEIN / Ion Channels / NMDAR
Function / homology
Function and homology information


cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / pons maturation / positive regulation of Schwann cell migration / regulation of cell communication / sensitization / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors ...cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / pons maturation / positive regulation of Schwann cell migration / regulation of cell communication / sensitization / 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 / response to other organism / protein localization to postsynaptic membrane / regulation of ARF protein signal transduction / fear response / apical dendrite / transmitter-gated monoatomic ion channel activity / positive regulation of inhibitory postsynaptic potential / suckling behavior / response to methylmercury / response to manganese ion / response to glycine / propylene metabolic process / response to carbohydrate / interleukin-1 receptor binding / cellular response to dsRNA / response to growth hormone / cellular response to lipid / negative regulation of dendritic spine maintenance / heterocyclic compound binding / positive regulation of glutamate secretion / regulation of monoatomic cation transmembrane transport / RAF/MAP kinase cascade / NMDA glutamate receptor activity / 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 / response to morphine / regulation of axonogenesis / neuromuscular process / calcium ion transmembrane import into cytosol / regulation of dendrite morphogenesis / protein heterotetramerization / male mating behavior / regulation of synapse assembly / glycine binding / response to amine / regulation of cAMP/PKA signal transduction / small molecule binding / parallel fiber to Purkinje cell synapse / receptor clustering / startle response / positive regulation of reactive oxygen species biosynthetic process / monoatomic cation transmembrane transport / behavioral response to pain / regulation of MAPK cascade / positive regulation of calcium ion transport into cytosol / regulation of postsynaptic membrane potential / response to magnesium ion / cellular response to glycine / associative learning / action potential / extracellularly glutamate-gated ion channel activity / excitatory synapse / response to electrical stimulus / positive regulation of dendritic spine maintenance / monoatomic cation transport / social behavior / regulation of neuronal synaptic plasticity / monoatomic ion channel complex / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of excitatory postsynaptic potential / long-term memory / detection of mechanical stimulus involved in sensory perception of pain / response to mechanical stimulus / synaptic cleft / neuron development / behavioral fear response / prepulse inhibition / phosphatase binding / multicellular organismal response to stress / positive regulation of synaptic transmission, glutamatergic / postsynaptic density, intracellular component / monoatomic cation channel activity / calcium ion homeostasis / response to fungicide / glutamate-gated receptor activity / cell adhesion molecule binding / regulation of neuron apoptotic process / regulation of long-term synaptic depression
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
: / CHOLESTEROL / Chem-POV / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsSteigerwald, R. / Furukawa, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH085926 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS111745 United States
CitationJournal: To Be Published / Year: 2025
Title: Mechanism of conductance control and neurosteroid binding in NMDA receptors
Authors: Steigerwald, R. / Furukawa, H.
History
DepositionMay 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: 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 2B
C: Glutamate receptor ionotropic, NMDA 1
D: Glutamate receptor ionotropic, NMDA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)387,65612
Polymers383,4504
Non-polymers4,2078
Water32418
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 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: 95225.883 Da / Num. of mol.: 2
Mutation: N61Q, N239D, N350Q, N471Q, N491Q, N771Q, R844Q, R845G, K846A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin1, Nmdar1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35439
#2: Protein Glutamate receptor ionotropic, NMDA 2B / GluN2B / Glutamate [NMDA] receptor subunit epsilon-2 / N-methyl D-aspartate receptor subtype 2B / ...GluN2B / Glutamate [NMDA] receptor subunit epsilon-2 / N-methyl D-aspartate receptor subtype 2B / NMDAR2B / NR2B


Mass: 96498.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2b / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q00960

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Non-polymers , 4 types, 26 molecules

#3: Chemical ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#4: Chemical
ChemComp-A1AFT / (5M)-5-(3-bromo-4-fluorophenyl)-6-ethynyl-3-[2-(3-fluoro-3-methylazetidin-1-yl)-2-oxoethyl]thieno[2,3-d]pyrimidin-4(3H)-one


Mass: 478.310 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H14BrF2N3O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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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: CELL / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Di-heteromeric GluN1a-2B NMDA receptor / Type: CELL / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Rattus norvegicus (Norway rat)
Buffer solutionpH: 7.5
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: 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: 600 nm
Image recordingElectron dose: 58.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 382882 / Symmetry type: POINT
RefinementHighest resolution: 3.34 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01113492
ELECTRON MICROSCOPYf_angle_d0.79918320
ELECTRON MICROSCOPYf_dihedral_angle_d8.7431912
ELECTRON MICROSCOPYf_chiral_restr0.0522078
ELECTRON MICROSCOPYf_plane_restr0.0062282

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