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- PDB-9unp: native NMDA receptor-GluN1/N2A/N2B-S2 in the closed state -

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Basic information

Entry
Database: PDB / ID: 9unp
Titlenative NMDA receptor-GluN1/N2A/N2B-S2 in the closed state
Components(Glutamate receptor ionotropic, NMDA ...) x 3
KeywordsMEMBRANE PROTEIN / native / NMDA receptor / inotropic ion channel / excitatory neurotransmitter / MEMBRANE / open state
Function / homology
Function and homology information


Assembly and cell surface presentation of NMDA receptors / EPHB-mediated forward signaling / Synaptic adhesion-like molecules / Unblocking of NMDA receptors, glutamate binding and activation / neurotransmitter receptor transport, plasma membrane to endosome / RAF/MAP kinase cascade / receptor recycling / sensory organ development / directional locomotion / regulation of cAMP/PKA signal transduction ...Assembly and cell surface presentation of NMDA receptors / EPHB-mediated forward signaling / Synaptic adhesion-like molecules / Unblocking of NMDA receptors, glutamate binding and activation / neurotransmitter receptor transport, plasma membrane to endosome / RAF/MAP kinase cascade / receptor recycling / sensory organ development / directional locomotion / regulation of cAMP/PKA signal transduction / pons maturation / positive regulation of Schwann cell migration / regulation of cell communication / sensitization / olfactory learning / serotonin metabolic process / fear response / dendritic branch / conditioned taste aversion / protein localization to postsynaptic membrane / regulation of ARF protein signal transduction / apical dendrite / suckling behavior / transmitter-gated monoatomic ion channel activity / sleep / interleukin-1 receptor binding / regulation of respiratory gaseous exchange / propylene metabolic process / response to glycine / dendritic spine organization / locomotion / regulation of NMDA receptor activity / negative regulation of dendritic spine maintenance / positive regulation of inhibitory postsynaptic potential / neurotransmitter receptor complex / heterocyclic compound binding / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / glutamate binding / voltage-gated monoatomic cation channel activity / neuromuscular process / ligand-gated sodium channel activity / glutamate receptor signaling pathway / transport vesicle membrane / regulation of axonogenesis / calcium ion transmembrane import into cytosol / monoatomic ion channel complex / response to morphine / positive regulation of glutamate secretion / male mating behavior / regulation of dendrite morphogenesis / protein heterotetramerization / positive regulation of reactive oxygen species biosynthetic process / regulation of synapse assembly / small molecule binding / glycine binding / dopamine metabolic process / startle response / receptor clustering / cellular response to zinc ion / response to lithium ion / parallel fiber to Purkinje cell synapse / regulation of neuronal synaptic plasticity / regulation of MAPK cascade / regulation of postsynaptic membrane potential / associative learning / behavioral response to pain / positive regulation of calcium ion transport into cytosol / extracellularly glutamate-gated ion channel activity / modulation of excitatory postsynaptic potential / positive regulation of dendritic spine maintenance / action potential / monoatomic cation transmembrane transport / positive regulation of protein targeting to membrane / detection of mechanical stimulus involved in sensory perception of pain / monoatomic cation transport / glutamate receptor binding / social behavior / ligand-gated monoatomic ion channel activity / behavioral fear response / positive regulation of synaptic transmission / prepulse inhibition / phosphatase binding / long-term memory / postsynaptic density, intracellular component / calcium ion homeostasis / synaptic cleft / monoatomic cation channel activity / adult locomotory behavior / glutamate-gated receptor activity / regulation of long-term synaptic depression / positive regulation of synaptic transmission, glutamatergic / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / neurogenesis / cell adhesion molecule binding / D2 dopamine receptor binding / ionotropic glutamate receptor signaling pathway / excitatory synapse
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 / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : ...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 / 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
GLUTAMIC ACID / GLYCINE / Chem-JC9 / Glutamate receptor ionotropic, NMDA 2A / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsYu, J. / Xu, R.S. / Ge, J.P.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nature / Year: 2026
Title: Conformational diversity and fully opening mechanism of native NMDA receptor.
Authors: Ruisheng Xu / Qiqi Jiang / Hongwei Xu / Lu Zhang / Xiangzi Hu / Zizhuo Lu / Huaqin Deng / Haolin Xiong / Sensen Zhang / Zhongwen Chen / Yifan Ge / Zhengjiang Zhu / Yaoyang Zhang / Yelin Chen ...Authors: Ruisheng Xu / Qiqi Jiang / Hongwei Xu / Lu Zhang / Xiangzi Hu / Zizhuo Lu / Huaqin Deng / Haolin Xiong / Sensen Zhang / Zhongwen Chen / Yifan Ge / Zhengjiang Zhu / Yaoyang Zhang / Yelin Chen / Jingpeng Ge / Jie Yu /
Abstract: N-methyl-D-aspartate receptors (NMDARs) are glutamate-gated ion channels that mediate excitatory neurotransmission throughout the brain. As obligate heterotetramers, their activation requires the ...N-methyl-D-aspartate receptors (NMDARs) are glutamate-gated ion channels that mediate excitatory neurotransmission throughout the brain. As obligate heterotetramers, their activation requires the binding of both glycine and glutamate. Although recent structural studies have provided insights into endogenous receptors from select brain regions, most previous work has relied on recombinant receptors and engineered constructs, which limits our understanding of native NMDARs across the whole brain. Here we identify and resolve ten distinct native NMDAR assemblies from the whole-brain tissue of female C57BL/6 mice using immunoaffinity purification, single-molecule total internal reflection fluorescence microscopy and cryo-electron microscopy. Analyses of the GluN1-GluN2A(S1), GluN1-GluN2A(S2), GluN1-GluN2A(S3), GluN1-GluN2B, GluN1-GluN2A-GluN2B(S1), GluN1-GluN2A-GluN2B(S2), GluN1-GluN2A-GluNX(S1), GluN1-GluN2A-GluNX(S2), GluN1-GluN2B-GluNX and GluN1-GluNX structures reveal that GluN2A is the most prevalent subunit across assemblies. Moreover, the substantial conformational flexibility observed in the GluN2A amino-terminal domain may explain its fast kinetics and dominant role in gating. Dynamic movements of S-ketamine were also captured at the channel vestibule, as was pore dilation in both the GluN1 and GluN2B subunits of a native GluN1-GluN2B receptor. The latter observation represents a previously unknown fully open state of NMDAR. Our large collection of heterogeneous NMDAR structures from whole brain reveals previously unrecognized properties of conformational diversity and channel dilation.
History
DepositionApr 24, 2025Deposition site: PDBJ / Processing site: PDBC
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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
C: Glutamate receptor ionotropic, NMDA 1
D: Glutamate receptor ionotropic, NMDA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)370,30025
Polymers366,0784
Non-polymers4,22121
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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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: 92408.602 Da / Num. of mol.: 2 / 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: 90335.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P35436
#3: 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: 90925.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q01097

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Sugars , 1 types, 16 molecules

#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.: 16 / Source method: obtained synthetically / Formula: C8H15NO6
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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Non-polymers , 3 types, 5 molecules

#5: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#6: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#7: Chemical ChemComp-JC9 / (2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one / Esketamine


Mass: 237.725 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16ClNO / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antidepressant*YM

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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 NMDA receptor-GluN1/N2A/N2B-S2 in the closed state
Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Mus musculus (house mouse)
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: TFS 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: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2cryoSPARCparticle selection
3PHENIX1.20.1_4487model refinement
14cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 248741 / Symmetry type: POINT
RefinementHighest resolution: 3.27 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00223661
ELECTRON MICROSCOPYf_angle_d0.42332308
ELECTRON MICROSCOPYf_dihedral_angle_d3.1183396
ELECTRON MICROSCOPYf_chiral_restr0.0393885
ELECTRON MICROSCOPYf_plane_restr0.0034087

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