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- EMDB-64354: native NMDA receptor-GluN1/N2B in the closed state -

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Basic information

Entry
Database: EMDB / ID: EMD-64354
Titlenative NMDA receptor-GluN1/N2B in the closed state
Map data
Sample
  • Complex: native NMDA receptor-GluN1/N2B in the closed 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
  • Ligand: GLYCINE
  • Ligand: GLUTAMIC ACID
  • Ligand: (2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one
Keywordsnative / NMDA receptor / ionotropic ion channel / excitatory neurotransmitter / MEMBRANE PROTEIN
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 / RAF/MAP kinase cascade / sensory organ development / sensitization / pons maturation / regulation of cAMP/PKA signal transduction / fear response ...Assembly and cell surface presentation of NMDA receptors / EPHB-mediated forward signaling / Synaptic adhesion-like molecules / Unblocking of NMDA receptors, glutamate binding and activation / RAF/MAP kinase cascade / sensory organ development / sensitization / pons maturation / regulation of cAMP/PKA signal transduction / fear response / positive regulation of Schwann cell migration / regulation of cell communication / protein localization to postsynaptic membrane / conditioned taste aversion / suckling behavior / olfactory learning / dendritic branch / regulation of ARF protein signal transduction / apical dendrite / transmitter-gated monoatomic ion channel activity / interleukin-1 receptor binding / regulation of respiratory gaseous exchange / propylene metabolic process / response to glycine / positive regulation of inhibitory postsynaptic potential / heterocyclic compound binding / negative regulation of dendritic spine maintenance / neuromuscular process / neurotransmitter receptor complex / NMDA glutamate receptor activity / regulation of monoatomic cation transmembrane transport / NMDA selective glutamate receptor complex / glutamate binding / regulation of axonogenesis / behavioral fear response / ligand-gated sodium channel activity / startle response / monoatomic ion channel complex / positive regulation of glutamate secretion / voltage-gated monoatomic cation channel activity / transport vesicle membrane / response to morphine / calcium ion transmembrane import into cytosol / regulation of synapse assembly / positive regulation of reactive oxygen species biosynthetic process / male mating behavior / protein heterotetramerization / regulation of dendrite morphogenesis / small molecule binding / behavioral response to pain / receptor clustering / glycine binding / positive regulation of calcium ion transport into cytosol / parallel fiber to Purkinje cell synapse / social behavior / regulation of neuronal synaptic plasticity / associative learning / regulation of postsynaptic membrane potential / regulation of MAPK cascade / extracellularly glutamate-gated ion channel activity / action potential / detection of mechanical stimulus involved in sensory perception of pain / positive regulation of dendritic spine maintenance / monoatomic cation transmembrane transport / glutamate receptor binding / monoatomic cation transport / positive regulation of synaptic transmission / ligand-gated monoatomic ion channel activity / prepulse inhibition / phosphatase binding / long-term memory / adult locomotory behavior / regulation of long-term neuronal synaptic plasticity / calcium ion homeostasis / postsynaptic density, intracellular component / monoatomic cation channel activity / sensory perception of pain / glutamate-gated receptor activity / regulation of long-term synaptic depression / response to amphetamine / positive regulation of synaptic transmission, glutamatergic / in utero embryonic development / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / visual learning / cell adhesion molecule binding / D2 dopamine receptor binding / synaptic cleft / ionotropic glutamate receptor binding / regulation of neuron apoptotic process / ionotropic glutamate receptor signaling pathway / learning / protein tyrosine kinase binding / excitatory synapse / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / excitatory postsynaptic potential / positive regulation of excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / protein serine/threonine kinase binding
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
Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 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-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64354.png

Downloads & links

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Map

FileDownload / File: emd_64354.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: 0.15
Minimum - Maximum-0.18570095 - 2.2545006
Average (Standard dev.)0.0074024615 (±0.029350433)
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 NMDA receptor-GluN1/N2B in the closed state

EntireName: native NMDA receptor-GluN1/N2B in the closed state
Components
  • Complex: native NMDA receptor-GluN1/N2B in the closed 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
  • Ligand: GLYCINE
  • Ligand: GLUTAMIC ACID
  • Ligand: (2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one

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Supramolecule #1: native NMDA receptor-GluN1/N2B in the closed state

SupramoleculeName: native NMDA receptor-GluN1/N2B in the closed 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: 92.408602 KDa
SequenceString: PKIVNIGAVL STRKHEQMFR EAVNQANKRH GSWKIQLNAT SVTHKPNAIQ MALSVCEDLI SSQVYAILVS HPPTPNDHFT PTPVSYTAG FYRIPVLGLT TRMSIYSDKS IHLSFLRTVP PYSHQSSVWF EMMRVYNWNH IILLVSDDHE GRAAQKRLET L LEERESKA ...String:
PKIVNIGAVL STRKHEQMFR EAVNQANKRH GSWKIQLNAT SVTHKPNAIQ MALSVCEDLI SSQVYAILVS HPPTPNDHFT PTPVSYTAG FYRIPVLGLT TRMSIYSDKS IHLSFLRTVP PYSHQSSVWF EMMRVYNWNH IILLVSDDHE GRAAQKRLET L LEERESKA EKVLQFDPGT KNVTALLMEA RDLEARVIIL SASEDDAATV YRAAAMLNMT GSGYVWLVGE REISGNALRY AP DGIIGLQ LINGKNESAH ISDAVGVVAQ AVHELLEKEN ITDPPRGCVG NTNIWKTGPL FKRVLMSSKY ADGVTGRVEF NED GDRKFA NYSIMNLQNR KLVQVGIYNG THVIPNDRKI IWPGGETEKP RGYQMSTRLK IVTIHQEPFV YVKPTMSDGT CKEE FTVNG DPVKKVICTG PNDTSPGSPR HTVPQCCYGF CVDLLIKLAR TMNFTYEVHL VADGKFGTQE RVNNSNKKEW NGMMG ELLS GQADMIVAPL TINNERAQYI EFSKPFKYQG LTILVKKEIP RSTLDSFMQP FQSTLWLLVG LSVHVVAVML YLLDRF SPF GRFKVNSEEE EEDALTLSSA MWFSWGVLLN SGIGEGAPRS FSARILGMVW AGFAMIIVAS YTANLAAFLV LDRPEER IT GINDPRLRNP SDKFIYATVK QSSVDIYFRR QVELSTMYRH MEKHNYESAA EAIQAVRDNK LHAFIWDSAV LEFEASQK C DLVTTGELFF RSGFGIGMRK DSPWKQNVSL SILKSHENGF MEDLDKTWVR YQECDSRSNA PATLTFENMA GVFMLVAGG IVAGIFLIFI EIAYKRHKDA R

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: 32 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #4: GLYCINE

MacromoleculeName: GLYCINE / type: ligand / ID: 4 / Number of copies: 2 / Formula: GLY
Molecular weightTheoretical: 75.067 Da
Chemical component information

ChemComp-GLY:
GLYCINE

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Macromolecule #5: GLUTAMIC ACID

MacromoleculeName: GLUTAMIC ACID / type: ligand / ID: 5 / Number of copies: 2 / Formula: GLU
Molecular weightTheoretical: 147.129 Da
Chemical component information

ChemComp-GLU:
GLUTAMIC ACID

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Macromolecule #6: (2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one

MacromoleculeName: (2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one
type: ligand / ID: 6 / Number of copies: 1 / Formula: JC9
Molecular weightTheoretical: 237.725 Da
Chemical component information

ChemComp-JC9:
(2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one

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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: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 169373
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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