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- EMDB-64337: native NMDAR receptor-GluN1/N2B in the inactive state -

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Basic information

Entry
Database: EMDB / ID: EMD-64337
Titlenative NMDAR receptor-GluN1/N2B in the inactive state
Map data
Sample
  • Complex: native NMDAR receptor-GluN1/N2B in the inactive state
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsnative / NMDA receptor / ionotropic ion channel / excitatory neurotransmitter / MEMBRANE PROTEIN
Function / homology
Function and homology information


Assembly and cell surface presentation of NMDA receptors / Synaptic adhesion-like molecules / EPHB-mediated forward signaling / Unblocking of NMDA receptors, glutamate binding and activation / RAF/MAP kinase cascade / sensory organ development / pons maturation / regulation of cAMP/PKA signal transduction / regulation of cell communication / positive regulation of Schwann cell migration ...Assembly and cell surface presentation of NMDA receptors / Synaptic adhesion-like molecules / EPHB-mediated forward signaling / Unblocking of NMDA receptors, glutamate binding and activation / RAF/MAP kinase cascade / sensory organ development / pons maturation / regulation of cAMP/PKA signal transduction / regulation of cell communication / positive regulation of Schwann cell migration / sensitization / olfactory learning / conditioned taste aversion / dendritic branch / fear response / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane / apical dendrite / regulation of ARF protein signal transduction / transmitter-gated monoatomic ion channel activity / suckling behavior / positive regulation of inhibitory postsynaptic potential / interleukin-1 receptor binding / propylene metabolic process / response to glycine / negative regulation of dendritic spine maintenance / heterocyclic compound binding / positive regulation of glutamate secretion / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / voltage-gated monoatomic cation channel activity / glutamate binding / neurotransmitter receptor complex / ligand-gated sodium channel activity / regulation of axonogenesis / calcium ion transmembrane import into cytosol / neuromuscular process / transport vesicle membrane / response to morphine / regulation of dendrite morphogenesis / protein heterotetramerization / male mating behavior / regulation of synapse assembly / glycine binding / small molecule binding / receptor clustering / startle response / ligand-gated monoatomic ion channel activity / positive regulation of reactive oxygen species biosynthetic process / parallel fiber to Purkinje cell synapse / behavioral response to pain / monoatomic cation transmembrane transport / regulation of MAPK cascade / monoatomic ion channel complex / positive regulation of calcium ion transport into cytosol / regulation of postsynaptic membrane potential / action potential / extracellularly glutamate-gated ion channel activity / associative learning / positive regulation of dendritic spine maintenance / regulation of neuronal synaptic plasticity / social behavior / monoatomic cation transport / glutamate receptor binding / prepulse inhibition / detection of mechanical stimulus involved in sensory perception of pain / long-term memory / positive regulation of synaptic transmission / phosphatase binding / positive regulation of synaptic transmission, glutamatergic / postsynaptic density, intracellular component / behavioral fear response / monoatomic cation channel activity / synaptic cleft / calcium ion homeostasis / glutamate-gated receptor activity / regulation of long-term synaptic depression / D2 dopamine receptor binding / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / cell adhesion molecule binding / dendrite membrane / excitatory synapse / ionotropic glutamate receptor binding / sensory perception of pain / ionotropic glutamate receptor signaling pathway / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / protein serine/threonine kinase binding / regulation of neuron apoptotic process / protein tyrosine kinase binding / synaptic membrane / sodium ion transmembrane transport / positive regulation of excitatory postsynaptic potential / response to amphetamine / hippocampal mossy fiber to CA3 synapse / adult locomotory behavior / learning / synaptic transmission, glutamatergic / excitatory postsynaptic potential
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
Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsYu J / Xu RS / Ge JP
Funding support China, 1 items
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 23, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64337.png

Downloads & links

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Map

FileDownload / File: emd_64337.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 422. Å		1.06 Å/pix.
x 400 pix.
= 422. Å		1.06 Å/pix.
x 400 pix.
= 422. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.44
Minimum - Maximum-0.4572511 - 2.7045255
Average (Standard dev.)0.008691069 (±0.05054511)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 421.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : native NMDAR receptor-GluN1/N2B in the inactive state

EntireName: native NMDAR receptor-GluN1/N2B in the inactive state
Components
  • Complex: native NMDAR receptor-GluN1/N2B in the inactive state
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: native NMDAR receptor-GluN1/N2B in the inactive state

SupramoleculeName: native NMDAR receptor-GluN1/N2B in the inactive state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Glutamate receptor ionotropic, NMDA 1

MacromoleculeName: Glutamate receptor ionotropic, NMDA 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 92.182305 KDa
SequenceString: IVNIGAVLST RKHEQMFREA VNQANKRHGS WKIQLNATSV THKPNAIQMA LSVCEDLISS QVYAILVSHP PTPNDHFTPT PVSYTAGFY RIPVLGLTTR MSIYSDKSIH LSFLRTVPPY SHQSSVWFEM MRVYNWNHII LLVSDDHEGR AAQKRLETLL E ERESKAEK ...String:
IVNIGAVLST RKHEQMFREA VNQANKRHGS WKIQLNATSV THKPNAIQMA LSVCEDLISS QVYAILVSHP PTPNDHFTPT PVSYTAGFY RIPVLGLTTR MSIYSDKSIH LSFLRTVPPY SHQSSVWFEM MRVYNWNHII LLVSDDHEGR AAQKRLETLL E ERESKAEK VLQFDPGTKN VTALLMEARD LEARVIILSA SEDDAATVYR AAAMLNMTGS GYVWLVGERE ISGNALRYAP DG IIGLQLI NGKNESAHIS DAVGVVAQAV HELLEKENIT DPPRGCVGNT NIWKTGPLFK RVLMSSKYAD GVTGRVEFNE DGD RKFANY SIMNLQNRKL VQVGIYNGTH VIPNDRKIIW PGGETEKPRG YQMSTRLKIV TIHQEPFVYV KPTMSDGTCK EEFT VNGDP VKKVICTGPN DTSPGSPRHT VPQCCYGFCV DLLIKLARTM NFTYEVHLVA DGKFGTQERV NNSNKKEWNG MMGEL LSGQ ADMIVAPLTI NNERAQYIEF SKPFKYQGLT ILVKKEIPRS TLDSFMQPFQ STLWLLVGLS VHVVAVMLYL LDRFSP FGR FKVNSEEEEE DALTLSSAMW FSWGVLLNSG IGEGAPRSFS ARILGMVWAG FAMIIVASYT ANLAAFLVLD RPEERIT GI NDPRLRNPSD KFIYATVKQS SVDIYFRRQV ELSTMYRHME KHNYESAAEA IQAVRDNKLH AFIWDSAVLE FEASQKCD L VTTGELFFRS GFGIGMRKDS PWKQNVSLSI LKSHENGFME DLDKTWVRYQ ECDSRSNAPA TLTFENMAGV FMLVAGGIV AGIFLIFIEI AYKRHKDAR

UniProtKB: Glutamate receptor ionotropic, NMDA 1

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Macromolecule #2: Glutamate receptor ionotropic, NMDA 2B

MacromoleculeName: Glutamate receptor ionotropic, NMDA 2B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 90.757672 KDa
SequenceString: SIGIAVILVG TSDEVAIKDA HEKDDFHHLS VVPRVELVAM NETDPKSIIT RICDLMSDRK IQGVVLADDT DQEAIAQILD FISAQTLTP ILGIHGGSSM IMADKDESSM FFQFGPSIEQ QASVMLNIME EYDWYIFSIV TTYFPGYQDF VNKIRSTIEN S FVGWELEE ...String:
SIGIAVILVG TSDEVAIKDA HEKDDFHHLS VVPRVELVAM NETDPKSIIT RICDLMSDRK IQGVVLADDT DQEAIAQILD FISAQTLTP ILGIHGGSSM IMADKDESSM FFQFGPSIEQ QASVMLNIME EYDWYIFSIV TTYFPGYQDF VNKIRSTIEN S FVGWELEE VLLLDMSLDD GDSKIQNQLK KLQSPIILLY CTKEEATYIF EVANSVGLTG YGYTWIVPSL VAGDTDTVPS EF PTGLISV SYDEWDYGLP ARVRDGIAII TTAASDMLSE HSFIPEPKSS CYNTHEKRIY QSNMLNRYLI NVTFEGRNLS FSE DGYQMH PKLVIILLNK ERKWERVGKW KDKSLQMKYY VWPRMCPETE EQEDDHLSIV TLEEAPFVIV ESVDPLSGTC MRNT VPCQK RIISENKTDE EPGYIKKCCK GFCIDILKKI SKSVKFTYDL YLVTNGKHGK KINGTWNGMI GEVVMKRAYM AVGSL TINE ERSEVVDFSV PFIETGISVM VSRSNGTVSP SAFLEPFSAD VWVMMFVMLL IVSAVAVFVF EYFSPVGYNR CLADGR EPG GPSFTIGKAI WLLWGLVFNN SVPVQNPKGT TSKIMVSVWA FFAVIFLASY TANLAAFMIQ EEYVDQVSGL SDKKFQR PN DFSPPFRFGT VPNGSTERNI RNNYAEMHAY MGKFNQRGVD DALLSLKTGK LDAFIYDAAV LNYMAGRDEG CKLVTIGS G KVFASTGYGI AIQKDSGWKR QVDLAILQLF GDGEMEELEA LWLTGICHNE KNEVMSSQLD IDNMAGVFYM LGAAMALSL ITFICEHLF

UniProtKB: Glutamate receptor ionotropic, NMDA 2B

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 17 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9bib

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 53147
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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