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- EMDB-70669: Closed state of Gly/Glu/24S-HC bound hGluN1a-2B NMDAR -

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Basic information

Entry
Database: EMDB / ID: EMD-70669
TitleClosed state of Gly/Glu/24S-HC bound hGluN1a-2B NMDAR
Map dataComposite map - Closed state of Gly/Glu/24S-HC bound hGluN1a-2B NMDAR
Sample
  • Complex: hGluN1a-2B NMDAR
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
  • Ligand: GLYCINE
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: GLUTAMIC ACID
  • Ligand: (10xi,13xi,24S)-14beta,17alpha-cholest-5-ene-3beta,24-diol
  • Ligand: water
KeywordsN-methyl-D-aspartate receptor / Closed state / 24S-HC / GluN2B / MEMBRANE PROTEIN
Function / homology
Function and homology information


glycine-gated cation channel activity / excitatory chemical synaptic transmission / Activated NTRK2 signals through FYN / Synaptic adhesion-like molecules / response to glycine / propylene metabolic process / negative regulation of dendritic spine maintenance / Assembly and cell surface presentation of NMDA receptors / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity ...glycine-gated cation channel activity / excitatory chemical synaptic transmission / Activated NTRK2 signals through FYN / Synaptic adhesion-like molecules / response to glycine / propylene metabolic process / negative regulation of dendritic spine maintenance / Assembly and cell surface presentation of NMDA receptors / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / Neurexins and neuroligins / glutamate binding / ligand-gated sodium channel activity / neurotransmitter receptor complex / glutamate receptor signaling pathway / calcium ion transmembrane import into cytosol / protein heterotetramerization / glycine binding / positive regulation of reactive oxygen species biosynthetic process / monoatomic cation transmembrane transport / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of calcium ion transport into cytosol / Long-term potentiation / excitatory synapse / monoatomic cation transport / regulation of neuronal synaptic plasticity / monoatomic ion channel complex / positive regulation of excitatory postsynaptic potential / synaptic cleft / positive regulation of synaptic transmission, glutamatergic / calcium ion homeostasis / MECP2 regulates neuronal receptors and channels / glutamate-gated calcium ion channel activity / EPHB-mediated forward signaling / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / sodium ion transmembrane transport / ionotropic glutamate receptor signaling pathway / Ras activation upon Ca2+ influx through NMDA receptor / synaptic membrane / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / brain development / postsynaptic density membrane / visual learning / regulation of synaptic plasticity / calcium ion transmembrane transport / long-term synaptic potentiation / terminal bouton / synaptic vesicle / late endosome / signaling receptor activity / amyloid-beta binding / RAF/MAP kinase cascade / response to ethanol / chemical synaptic transmission / dendritic spine / postsynaptic membrane / learning or memory / cytoskeleton / calmodulin binding / lysosome / neuron projection / postsynaptic density / dendrite / calcium ion binding / synapse / endoplasmic reticulum membrane / protein-containing complex binding / cell surface / positive regulation of transcription by RNA polymerase II / zinc ion binding / plasma membrane / cytoplasm
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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHyunook K / Hiro F
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH085926 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS111745 United States
CitationJournal: Nature / Year: 2025
Title: Mechanism of conductance control and neurosteroid binding in NMDA receptors
Authors: Hyunook K / Hiro F
History
DepositionMay 16, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70669.png

Downloads & links

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Map

FileDownload / File: emd_70669.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map - Closed state of Gly/Glu/24S-HC bound hGluN1a-2B NMDAR
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 330.8 Å		0.83 Å/pix.
x 400 pix.
= 330.8 Å		0.83 Å/pix.
x 400 pix.
= 330.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.13386075 - 0.6447323
Average (Standard dev.)0.0022820567 (±0.010068404)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 330.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : hGluN1a-2B NMDAR

EntireName: hGluN1a-2B NMDAR
Components
  • Complex: hGluN1a-2B NMDAR
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
  • Ligand: GLYCINE
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: GLUTAMIC ACID
  • Ligand: (10xi,13xi,24S)-14beta,17alpha-cholest-5-ene-3beta,24-diol
  • Ligand: water

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Supramolecule #1: hGluN1a-2B NMDAR

SupramoleculeName: hGluN1a-2B NMDAR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 387 KDa

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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: Homo sapiens (human)
Molecular weightTheoretical: 93.14932 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: ARAASDPKIV NIGAVLSTRK HEQMFREAVN QANKRHGSWK IQLNATSVTH KPNAIQMALS VCEDLISSQV YAILVSHPPT PNDHFTPTP VSYTAGFYRI PVLGLTTRMS IYSDKSIHLS FLRTVPPYSH QSSVWFEMMR VYSWNHIILL VSDDHEGRAA Q KRLETLLE ...String:
ARAASDPKIV NIGAVLSTRK HEQMFREAVN QANKRHGSWK IQLNATSVTH KPNAIQMALS VCEDLISSQV YAILVSHPPT PNDHFTPTP VSYTAGFYRI PVLGLTTRMS IYSDKSIHLS FLRTVPPYSH QSSVWFEMMR VYSWNHIILL VSDDHEGRAA Q KRLETLLE ERESKAEKVL QFDPGTKNVT ALLMEAKELE ARVIILSASE DDAATVYRAA AMLNMTGSGY VWLVGEREIS GN ALRYAPD GILGLQLING KNESAHISDA VGVVAQAVHE LLEKENITDP PRGCVGNTNI WKTGPLFKRV LMSSKYADGV TGR VEFNED GDRKFANYSI MNLQNRKLVQ VGIYNGTHVI PNDRKIIWPG GETEKPRGYQ MSTRLKIVTI HQEPFVYVKP TLSD GTCKE EFTVNGDPVK KVICTGPNDT SPGSPRHTVP QCCYGFCIDL LIKLARTMNF TYEVHLVADG KFGTQERVNN SNKKE WNGM MGELLSGQAD MIVAPLTINN ERAQYIEFSK PFKYQGLTIL VKKEIPRSTL DSFMQPFQST LWLLVGLSVH VVAVML YLL DRFSPFGRFK VNSEEEEEDA LTLSSAMWFS WGVLLNSGIG EGAPRSFSAR ILGMVWAGFA MIIVASYTAN LAAFLVL DR PEERITGIND PRLRNPSDKF IYATVKQSSV DIYFRRQVEL STMYRHMEKH NYESAAEAIQ AVRDNKLHAF IWDSAVLE F EASQKCDLVT TGELFFRSGF GIGMRKDSPW KQNVSLSILK SHENGFMEDL DKTWVRYQEC DSRSNAPATL TFENMAGVF MLVAGGIVAG IFLIFIEIAY KRHKDANGAQ

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 / Details: Twin-strep tag at its N-terminus / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 96.393797 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: WSHPQFEKGG GSGGGSGGSA WSHPQFEKGA LVPRGRSQKS PPSIGIAVIL VGTSDEVAIK DAHEKDDFHH LSVVPRVELV AMNETDPKS IITRICDLMS DRKIQGVVFA DDTDQEAIAQ ILDFISAQTL TPILGIHGGS SMIMADKDES SMFFQFGPSI E QQASVMLN ...String:
WSHPQFEKGG GSGGGSGGSA WSHPQFEKGA LVPRGRSQKS PPSIGIAVIL VGTSDEVAIK DAHEKDDFHH LSVVPRVELV AMNETDPKS IITRICDLMS DRKIQGVVFA DDTDQEAIAQ ILDFISAQTL TPILGIHGGS SMIMADKDES SMFFQFGPSI E QQASVMLN IMEEYDWYIF SIVTTYFPGY QDFVNKIRST IENSFVGWEL EEVLLLDMSL DDGDSKIQNQ LKKLQSPIIL LY CTKEEAT YIFEVANSVG LTGYGYTWIV PSLVAGDTDT VPAEFPTGLI SVSYDEWDYG LPARVRDGIA IITTAASDML SEH SFIPEP KSSCYNTHEK RIYQSNMLNR YLINVTFEGR NLSFSEDGYQ MHPKLVIILL NKERKWERVG KWKDKSLQMK YYVW PRMCP ETEEQEDDHL SIVTLEEAPF VIVESVDPLS GTCMRNTVPC QKRIVTENKT DEEPGYIKKC CKGFCIDILK KISKS VKFT YDLYLVTNGK HGKKINGTWN GMIGEVVMKR AYMAVGSLTI NEERSEVVDF SVPFIETGIS VMVSRSNGTV SPSAFL EPF SADVWVMMFV MLLIVSAVAV FVFEYFSPVG YNRSLADGRE PGGPSFTIGK AIWLLWGLVF NNSVPVQNPK GTTSKIM VS VWAFFAVIFL ASYTANLAAF MIQEEYVDQV SGLSDKKFQR PNDFSPPFRF GTVPNGSTER NIRNNYAEMH AYMGKFNQ R GVDDALLSLK TGKLDAFIYD AAVLNYMAGR DEGCKLVTIG SGKVFASTGY GIAIQKDSGW KRQVDLAILQ LFGDGEMEE LEALWLTGIC HNEKNEVMSS QLDIDNMAGV FYMLGAAMAL SLITFISEHL FYWQFRHSFM G

UniProtKB: Glutamate receptor ionotropic, NMDA 2B

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Macromolecule #3: GLYCINE

MacromoleculeName: GLYCINE / type: ligand / ID: 3 / Number of copies: 2 / Formula: GLY
Molecular weightTheoretical: 75.067 Da
Chemical component information

ChemComp-GLY:
GLYCINE

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Macromolecule #4: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 4 / Number of copies: 8 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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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: (10xi,13xi,24S)-14beta,17alpha-cholest-5-ene-3beta,24-diol

MacromoleculeName: (10xi,13xi,24S)-14beta,17alpha-cholest-5-ene-3beta,24-diol
type: ligand / ID: 6 / Number of copies: 2 / Formula: A1CE1
Molecular weightTheoretical: 402.653 Da

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 13 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration3 mg/mL
BufferpH: 8.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 14 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.0 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: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4468308
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 243459
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial model
PDB IDChain

7saa

chain_id: A, source_name: PDB, initial_model_type: experimental model

7saa

chain_id: B, source_name: PDB, initial_model_type: experimental model

7saa

chain_id: C, source_name: PDB, initial_model_type: experimental model

7saa

chain_id: D, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9ooq:
Closed state of Gly/Glu/24S-HC bound hGluN1a-2B NMDAR

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