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- EMDB-64360: native NMDA receptor-GluN1/N2A/2B in inactive state -

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Basic information

Entry
Database: EMDB / ID: EMD-64360
Titlenative NMDA receptor-GluN1/N2A/2B in inactive state
Map data
Sample
  • Complex: native NMDA receptor-GluN1/N2A/2B in inactive state
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2A
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: GLYCINE
  • Ligand: GLUTAMIC ACID
Keywordsnative / NMDA receptor / ion channel / excitatory neurotransmitter / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
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 / neurotransmitter receptor transport, plasma membrane to endosome / RAF/MAP kinase cascade / receptor recycling / sensory organ development / directional locomotion / pons maturation ...Assembly and cell surface presentation of NMDA receptors / Synaptic adhesion-like molecules / EPHB-mediated forward signaling / 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 / 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 / serotonin metabolic process / regulation of ARF protein signal transduction / transmitter-gated monoatomic ion channel activity / suckling behavior / positive regulation of inhibitory postsynaptic potential / interleukin-1 receptor binding / sleep / propylene metabolic process / response to glycine / locomotion / dendritic spine organization / 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 / glutamate receptor signaling pathway / 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 / cellular response to zinc ion / ligand-gated monoatomic ion channel activity / dopamine metabolic process / positive regulation of reactive oxygen species biosynthetic process / parallel fiber to Purkinje cell synapse / response to lithium ion / 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 / modulation of excitatory postsynaptic potential / associative learning / positive regulation of dendritic spine maintenance / regulation of neuronal synaptic plasticity / social behavior / positive regulation of protein targeting to membrane / 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 / neurogenesis / presynaptic active zone membrane / cell adhesion molecule binding / dendrite membrane / excitatory synapse / ionotropic glutamate receptor binding / sensory perception of pain
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 2A / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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 24, 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_64360.png

Downloads & links

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Map

FileDownload / File: emd_64360.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: 0.27
Minimum - Maximum-1.9771957 - 6.5981884
Average (Standard dev.)0.013680605 (±0.07523915)
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/N2A/2B in inactive state

EntireName: native NMDA receptor-GluN1/N2A/2B in inactive state
Components
  • Complex: native NMDA receptor-GluN1/N2A/2B in inactive state
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2A
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: GLYCINE
  • Ligand: GLUTAMIC ACID

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Supramolecule #1: native NMDA receptor-GluN1/N2A/2B in inactive state

SupramoleculeName: native NMDA receptor-GluN1/N2A/2B in inactive state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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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: 92.083203 KDa
SequenceString: KIVNIGAVLS TRKHEQMFRE AVNQANKRHG SWKIQLNATS VTHKPNAIQM ALSVCEDLIS SQVYAILVSH PPTPNDHFTP TPVSYTAGF YRIPVLGLTT RMSIYSDKSI HLSFLRTVPP YSHQSSVWFE MMRVYNWNHI ILLVSDDHEG RAAQKRLETL L EERESKAE ...String:
KIVNIGAVLS TRKHEQMFRE AVNQANKRHG SWKIQLNATS VTHKPNAIQM ALSVCEDLIS SQVYAILVSH PPTPNDHFTP TPVSYTAGF YRIPVLGLTT RMSIYSDKSI HLSFLRTVPP YSHQSSVWFE MMRVYNWNHI ILLVSDDHEG RAAQKRLETL L EERESKAE KVLQFDPGTK NVTALLMEAR DLEARVIILS ASEDDAATVY RAAAMLNMTG SGYVWLVGER EISGNALRYA PD GIIGLQL INGKNESAHI SDAVGVVAQA VHELLEKENI TDPPRGCVGN TNIWKTGPLF KRVLMSSKYA DGVTGRVEFN EDG DRKFAN YSIMNLQNRK LVQVGIYNGT HVIPNDRKII WPGGETEKPR GYQMSTRLKI VTIHQEPFVY VKPTMSDGTC KEEF TVNGD PVKKVICTGP NDTSPGSPRH TVPQCCYGFC VDLLIKLART MNFTYEVHLV ADGKFGTQER VNNSNKKEWN GMMGE LLSG QADMIVAPLT INNERAQYIE FSKPFKYQGL TILVKKEIPR STLDSFMQPF QSTLWLLVGL SVHVVAVMLY LLDRFS PFG RFKVNSEEEE EDALTLSSAM WFSWGVLLNS GIGEGAPRSF SARILGMVWA GFAMIIVASY TANLAAFLVL DRPEERI TG INDPRLRNPS DKFIYATVKQ SSVDIYFRRQ VELSTMYRHM EKHNYESAAE AIQAVRDNKL HAFIWDSAVL EFEASQKC D LVTTGELFFR SGFGIGMRKD SPWKQNVSLS ILKSHENGFM EDLDKTWVRY QECDSRSNAP ATLTFENMAG VFMLVAGGI VAGIFLIFIE IAYKRHKD

UniProtKB: Glutamate receptor ionotropic, NMDA 1

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Macromolecule #2: Glutamate receptor ionotropic, NMDA 2A

MacromoleculeName: Glutamate receptor ionotropic, NMDA 2A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 90.708734 KDa
SequenceString: LNIAVLLGHS HDVTERELRN LWGPEQATGL PLDVNVVALL MNRTDPKSLI THVCDLMSGA RIHGLVFGDD TDQEAVAQML DFISSQTFI PILGIHGGAS MIMADKDPTS TFFQFGASIQ QQATVMLKIM QDYDWHVFSL VTTIFPGYRD FISFIKTTVD N SFVGWDMQ ...String:
LNIAVLLGHS HDVTERELRN LWGPEQATGL PLDVNVVALL MNRTDPKSLI THVCDLMSGA RIHGLVFGDD TDQEAVAQML DFISSQTFI PILGIHGGAS MIMADKDPTS TFFQFGASIQ QQATVMLKIM QDYDWHVFSL VTTIFPGYRD FISFIKTTVD N SFVGWDMQ NVITLDTSFE DAKTQVQLKK IHSSVILLYC SKDEAVLILS EARSLGLTGY DFFWIVPSLV SGNTELIPKE FP SGLISVS YDDWDYSLEA RVRDGLGILT TAASSMLEKF SYIPEAKASC YGQTEKPETP LHTLHQFMVN VTWDGKDLSF TEE GYQVHP RLVVIVLNKD REWEKVGKWE NQTLSLRHAV WPRYKSFSDC EPDDNHLSIV TLEEAPFVIV EDIDPLTETC VRNT VPCRK FVKINNSTNE GMNVKKCCKG FCIDILKKLS RTVKFTYDLY LVTNGKHGKK VNNVWNGMIG EVVYQRAVMA VGSLT INEE RSEVVDFSVP FVETGISVMV SRSNGTVSPS AFLEPFSASV WVMMFVMLLI VSAIAVFVFE YFSPVGYNRN LAKGKA PHG PSFTIGKAIW LLWGLVFNNS VPVQNPKGTT SKIMVSVWAF FAVIFLASYT ANLAAFMIQE EFVDQVTGLS DKKFQRP HD YSPPFRFGTV PNGSTERNIR NNYPYMHQYM TKFNQRGVED ALVSLKTGKL DAFIYDAAVL NYKAGRDEGC KLVTIGSG Y IFATTGYGIA LQKGSPWKRQ IDLALLQFVG DGEMEELETL WLTGICHNEK NEVMSSQLDI DNMAGVFYML AAAMALSLI TFIWEHLF

UniProtKB: Glutamate receptor ionotropic, NMDA 2A

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Macromolecule #3: Glutamate receptor ionotropic, NMDA 2B

MacromoleculeName: Glutamate receptor ionotropic, NMDA 2B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 90.925859 KDa
SequenceString: APSIGIAVIL VGTSDEVAIK DAHEKDDFHH LSVVPRVELV AMNETDPKSI ITRICDLMSD RKIQGVVLAD DTDQEAIAQI LDFISAQTL TPILGIHGGS SMIMADKDES SMFFQFGPSI EQQASVMLNI MEEYDWYIFS IVTTYFPGYQ DFVNKIRSTI E NSFVGWEL ...String:
APSIGIAVIL VGTSDEVAIK DAHEKDDFHH LSVVPRVELV AMNETDPKSI ITRICDLMSD RKIQGVVLAD DTDQEAIAQI LDFISAQTL TPILGIHGGS SMIMADKDES SMFFQFGPSI EQQASVMLNI MEEYDWYIFS IVTTYFPGYQ DFVNKIRSTI E NSFVGWEL EEVLLLDMSL DDGDSKIQNQ LKKLQSPIIL LYCTKEEATY IFEVANSVGL TGYGYTWIVP SLVAGDTDTV PS EFPTGLI SVSYDEWDYG LPARVRDGIA IITTAASDML SEHSFIPEPK SSCYNTHEKR IYQSNMLNRY LINVTFEGRN LSF SEDGYQ MHPKLVIILL NKERKWERVG KWKDKSLQMK YYVWPRMCPE TEEQEDDHLS IVTLEEAPFV IVESVDPLSG TCMR NTVPC QKRIISENKT DEEPGYIKKC CKGFCIDILK KISKSVKFTY DLYLVTNGKH GKKINGTWNG MIGEVVMKRA YMAVG SLTI NEERSEVVDF SVPFIETGIS VMVSRSNGTV SPSAFLEPFS ADVWVMMFVM LLIVSAVAVF VFEYFSPVGY NRCLAD GRE PGGPSFTIGK AIWLLWGLVF NNSVPVQNPK GTTSKIMVSV WAFFAVIFLA SYTANLAAFM IQEEYVDQVS GLSDKKF QR PNDFSPPFRF GTVPNGSTER NIRNNYAEMH AYMGKFNQRG VDDALLSLKT GKLDAFIYDA AVLNYMAGRD EGCKLVTI G SGKVFASTGY GIAIQKDSGW KRQVDLAILQ LFGDGEMEEL EALWLTGICH NEKNEVMSSQ LDIDNMAGVF YMLGAAMAL SLITFICEHL F

UniProtKB: Glutamate receptor ionotropic, NMDA 2B

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 20 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #5: GLYCINE

MacromoleculeName: GLYCINE / type: ligand / ID: 5 / Number of copies: 2 / Formula: GLY
Molecular weightTheoretical: 75.067 Da
Chemical component information

ChemComp-GLY:
GLYCINE

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Macromolecule #6: GLUTAMIC ACID

MacromoleculeName: GLUTAMIC ACID / type: ligand / ID: 6 / Number of copies: 2 / Formula: GLU
Molecular weightTheoretical: 147.129 Da
Chemical component information

ChemComp-GLU:
GLUTAMIC ACID

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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: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 585019
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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