[English] 日本語
Yorodumi
- EMDB-64359: native NMDA receptor-GluN1/N2A/N2B-S2 in the closed state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-64359
Titlenative NMDA receptor-GluN1/N2A/N2B-S2 in the closed state
Map data
Sample
  • Complex: native NMDA receptor-GluN1/N2A/N2B-S2 in the closed 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
  • Ligand: (2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one
Keywordsnative / NMDA receptor / inotropic ion channel / excitatory neurotransmitter / MEMBRANE / open state / 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 / 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 / suckling behavior / fear response / dendritic branch / protein localization to postsynaptic membrane / conditioned taste aversion / regulation of ARF protein signal transduction / apical dendrite / transmitter-gated monoatomic ion channel activity / sleep / serotonin metabolic process / 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 / neuromuscular process / neurotransmitter receptor complex / heterocyclic compound binding / NMDA glutamate receptor activity / regulation of monoatomic cation transmembrane transport / cellular response to zinc ion / NMDA selective glutamate receptor complex / glutamate binding / voltage-gated monoatomic cation channel activity / ligand-gated sodium channel activity / response to morphine / transport vesicle membrane / regulation of axonogenesis / monoatomic ion channel complex / calcium ion transmembrane import into cytosol / 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 / startle response / small molecule binding / glycine binding / dopamine metabolic process / receptor clustering / response to lithium ion / parallel fiber to Purkinje cell synapse / glutamate receptor signaling pathway / associative learning / social behavior / behavioral response to pain / regulation of neuronal synaptic plasticity / positive regulation of calcium ion transport into cytosol / behavioral fear response / regulation of MAPK cascade / regulation of postsynaptic membrane potential / action potential / extracellularly glutamate-gated ion channel activity / modulation of excitatory postsynaptic potential / positive regulation of dendritic spine maintenance / monoatomic cation transmembrane transport / detection of mechanical stimulus involved in sensory perception of pain / positive regulation of protein targeting to membrane / monoatomic cation transport / glutamate receptor binding / ligand-gated monoatomic ion channel activity / prepulse inhibition / positive regulation of synaptic transmission / calcium ion homeostasis / long-term memory / phosphatase binding / postsynaptic density, intracellular component / synaptic cleft / monoatomic cation channel activity / adult locomotory behavior / neurogenesis / 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 / sensory perception of pain / cell adhesion molecule binding / D2 dopamine receptor binding / regulation of neuron apoptotic process
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 2A / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 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-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_64359.png

Downloads & links

-
Map

FileDownload / File: emd_64359.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-0.22704385 - 4.9075565
Average (Standard dev.)0.007368104 (±0.028227475)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Sample components

-
Entire : native NMDA receptor-GluN1/N2A/N2B-S2 in the closed state

EntireName: native NMDA receptor-GluN1/N2A/N2B-S2 in the closed state
Components
  • Complex: native NMDA receptor-GluN1/N2A/N2B-S2 in the closed 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
  • Ligand: (2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one

-
Supramolecule #1: native NMDA receptor-GluN1/N2A/N2B-S2 in the closed state

SupramoleculeName: native NMDA receptor-GluN1/N2A/N2B-S2 in the closed state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mus musculus (house mouse)

-
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

-
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: 90.33525 KDa
SequenceString: NIAVLLGHSH DVTERELRNL WGPEQATGLP LDVNVVALLM NRTDPKSLIT HVCDLMSGAR IHGLVFGDDT DQEAVAQMLD FISSQTFIP ILGIHGGASM IMADKDPTST FFQFGASIQQ QATVMLKIMQ DYDWHVFSLV TTIFPGYRDF ISFIKTTVDN S FVGWDMQN ...String:
NIAVLLGHSH DVTERELRNL WGPEQATGLP LDVNVVALLM NRTDPKSLIT HVCDLMSGAR IHGLVFGDDT DQEAVAQMLD FISSQTFIP ILGIHGGASM IMADKDPTST FFQFGASIQQ QATVMLKIMQ DYDWHVFSLV TTIFPGYRDF ISFIKTTVDN S FVGWDMQN VITLDTSFED AKTQVQLKKI HSSVILLYCS KDEAVLILSE ARSLGLTGYD FFWIVPSLVS GNTELIPKEF PS GLISVSY DDWDYSLEAR VRDGLGILTT AASSMLEKFS YIPEAKASCY GQTEKPETPL HTLHQFMVNV TWDGKDLSFT EEG YQVHPR LVVIVLNKDR EWEKVGKWEN QTLSLRHAVW PRYKSFSDCE PDDNHLSIVT LEEAPFVIVE DIDPLTETCV RNTV PCRKF VKINNSTNEG MNVKKCCKGF CIDILKKLSR TVKFTYDLYL VTNGKHGKKV NNVWNGMIGE VVYQRAVMAV GSLTI NEER SEVVDFSVPF VETGISVMVS RSNGTVSPSA FLEPFSASVW VMMFVMLLIV SAIAVFVFEY FSPVGYNRNL AKGKAP HGP SFTIGKAIWL LWGLVFNNSV PVQNPKGTTS KIMVSVWAFF AVIFLASYTA NLAAFMIQEE FVDQVTGLSD KKFQRPH DY SPPFRFGTVP NGSTERNIRN NYPYMHQYMT KFNQRGVEDA LVSLKTGKLD AFIYDAAVLN YKAGRDEGCK LVTIGSGY I FATTGYGIAL QKGSPWKRQI DLALLQFVGD GEMEELETLW LTGICHNEKN EVMSSQLDID NMAGVFYMLA AAMALSLIT FIWEH

UniProtKB: Glutamate receptor ionotropic, NMDA 2A

-
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

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 16 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
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

-
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

-
Macromolecule #7: (2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one

MacromoleculeName: (2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one
type: ligand / ID: 7 / 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 / medication, antidepressant*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
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

+
Image processing

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

7eu7

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 248741
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more