[English] 日本語
Yorodumi
- EMDB-72081: Native GluN1/GluN2B in complex with 5F11 Fab (class 4), glycine a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-72081
TitleNative GluN1/GluN2B in complex with 5F11 Fab (class 4), glycine and glutamate-bound state
Map data
Sample
  • Complex: Native GluN1/GluN2B in complex with 5F11 Fab (class 4), glycine and glutamate-bound state
    • Protein or peptide: Heavy chain of GluN1-specific monoclonal Fab fragment, termed 5F11
    • Protein or peptide: Light chain of GluN1-specific monoclonal Fab fragment, termed 5F11
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsligand-gated ion channel / NMDA / antibody / native / TRANSPORT 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 cell communication / olfactory learning / conditioned taste aversion ...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 cell communication / olfactory learning / conditioned taste aversion / regulation of respiratory gaseous exchange / fear response / protein localization to postsynaptic membrane / suckling behavior / propylene metabolic process / negative regulation of dendritic spine maintenance / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / glutamate binding / neurotransmitter receptor complex / ligand-gated sodium channel activity / response to morphine / regulation of axonogenesis / neuromuscular process / calcium ion transmembrane import into cytosol / regulation of dendrite morphogenesis / transport vesicle membrane / protein heterotetramerization / male mating behavior / regulation of synapse assembly / regulation of cAMP/PKA signal transduction / glycine binding / startle response / monoatomic cation transmembrane transport / behavioral response to pain / regulation of postsynaptic membrane potential / associative learning / social behavior / regulation of neuronal synaptic plasticity / monoatomic cation transport / positive regulation of excitatory postsynaptic potential / long-term memory / detection of mechanical stimulus involved in sensory perception of pain / prepulse inhibition / positive regulation of synaptic transmission, glutamatergic / behavioral fear response / monoatomic cation channel activity / calcium ion homeostasis / regulation of neuron apoptotic process / glutamate-gated calcium ion channel activity / sensory perception of pain / ionotropic glutamate receptor signaling pathway / sodium ion transmembrane transport / synaptic membrane / response to amphetamine / adult locomotory behavior / learning / regulation of membrane potential / synaptic transmission, glutamatergic / excitatory postsynaptic potential / regulation of long-term neuronal synaptic plasticity / neuron cellular homeostasis / postsynaptic density membrane / cerebral cortex development / regulation of synaptic plasticity / visual learning / calcium ion transmembrane transport / calcium channel activity / memory / long-term synaptic potentiation / intracellular calcium ion homeostasis / synaptic vesicle / synaptic vesicle membrane / calcium ion transport / late endosome / growth cone / presynaptic membrane / response to ethanol / dendritic spine / chemical synaptic transmission / in utero embryonic development / negative regulation of neuron apoptotic process / postsynaptic membrane / transcription by RNA polymerase II / learning or memory / cytoskeleton / calmodulin binding / lysosome / neuron projection / postsynapse / postsynaptic density / positive regulation of apoptotic process / signaling receptor binding / calcium ion binding / synapse / dendrite / endoplasmic reticulum membrane / glutamatergic synapse / cell surface
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: 5.36 Å
AuthorsKim J / Gouaux E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
CitationJournal: To Be Published
Title: Native GluN1/GluN2B in complex with 5F11 Fab (class 4), glycine and glutamate-bound state
Authors: Kim J / Gouaux E
History
DepositionAug 11, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_72081.png

Downloads & links

-
Map

FileDownload / File: emd_72081.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 336 pix.
= 468.384 Å		1.39 Å/pix.
x 336 pix.
= 468.384 Å		1.39 Å/pix.
x 336 pix.
= 468.384 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.394 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.03798007 - 0.0948815
Average (Standard dev.)0.00016686859 (±0.0034738695)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 468.38403 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Sharpen map

Fileemd_72081_additional_1.map
AnnotationSharpen map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_72081_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_72081_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Native GluN1/GluN2B in complex with 5F11 Fab (class 4), glycine a...

EntireName: Native GluN1/GluN2B in complex with 5F11 Fab (class 4), glycine and glutamate-bound state
Components
  • Complex: Native GluN1/GluN2B in complex with 5F11 Fab (class 4), glycine and glutamate-bound state
    • Protein or peptide: Heavy chain of GluN1-specific monoclonal Fab fragment, termed 5F11
    • Protein or peptide: Light chain of GluN1-specific monoclonal Fab fragment, termed 5F11
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Native GluN1/GluN2B in complex with 5F11 Fab (class 4), glycine a...

SupramoleculeName: Native GluN1/GluN2B in complex with 5F11 Fab (class 4), glycine and glutamate-bound state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 617 KDa

-
Macromolecule #1: Heavy chain of GluN1-specific monoclonal Fab fragment, termed 5F11

MacromoleculeName: Heavy chain of GluN1-specific monoclonal Fab fragment, termed 5F11
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 29.432527 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVSAIVLYVL LAAAAHSAFA QGQMQQSGAE LVKPGASVKL SCKTSGFSFS TSYINWLKQK PGQSLEWIAW IYAGTDGTSY NQKFTDKAQ LTVDTSSSTA YMQFSSLTTD DSAIYYCARE GIYYGNYAGF TYWGQGTLVT VSAAKTTPPS VYPLAPGSAA Q TNSMVTLG ...String:
MVSAIVLYVL LAAAAHSAFA QGQMQQSGAE LVKPGASVKL SCKTSGFSFS TSYINWLKQK PGQSLEWIAW IYAGTDGTSY NQKFTDKAQ LTVDTSSSTA YMQFSSLTTD DSAIYYCARE GIYYGNYAGF TYWGQGTLVT VSAAKTTPPS VYPLAPGSAA Q TNSMVTLG CLVKGYFPEP VTVTWNSGSL SSGVHTFPAV LQSDLYTLSS SVTVPSSTWP SETVTCNVAH PASSTKVDKK LV PRGSAAA AGTGSGGGDY KDHDGDYKDH DIDYKDDDDK

-
Macromolecule #2: Light chain of GluN1-specific monoclonal Fab fragment, termed 5F11

MacromoleculeName: Light chain of GluN1-specific monoclonal Fab fragment, termed 5F11
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.909961 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVSAIVLYVL LAAAAHSAFA DIVMTQSPSS LAVTAGEKVT MRCKSSQSLL WSVNQNNYLS WYQQKQGQPP KLLIYGASIR ESWVPDRFT GSGSGTDFTL TISNVHAEDL AVYYCQHNHG SFLPYTFGGG TKLEIKRADA APTVSIFPPS SEQLTSGGAS V VCFLNNFY ...String:
MVSAIVLYVL LAAAAHSAFA DIVMTQSPSS LAVTAGEKVT MRCKSSQSLL WSVNQNNYLS WYQQKQGQPP KLLIYGASIR ESWVPDRFT GSGSGTDFTL TISNVHAEDL AVYYCQHNHG SFLPYTFGGG TKLEIKRADA APTVSIFPPS SEQLTSGGAS V VCFLNNFY PKDINVKWKI DGSERQNGVL NSWTDQDSKD STYSMSSTLT LTKDEYERHN SYTCEATHKT STSPIVKSFN RN ECSN

-
Macromolecule #3: Glutamate receptor ionotropic, NMDA 1

MacromoleculeName: Glutamate receptor ionotropic, NMDA 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 105.61782 KDa
SequenceString: MSTMHLLTFA LLFSCSFARA ACDPKIVNIG AVLSTRKHEQ MFREAVNQAN KRHGSWKIQL NATSVTHKPN AIQMALSVCE DLISSQVYA ILVSHPPTPN DHFTPTPVSY TAGFYRIPVL GLTTRMSIYS DKSIHLSFLR TVPPYSHQSS VWFEMMRVYN W NHIILLVS ...String:
MSTMHLLTFA LLFSCSFARA ACDPKIVNIG AVLSTRKHEQ MFREAVNQAN KRHGSWKIQL NATSVTHKPN AIQMALSVCE DLISSQVYA ILVSHPPTPN DHFTPTPVSY TAGFYRIPVL GLTTRMSIYS DKSIHLSFLR TVPPYSHQSS VWFEMMRVYN W NHIILLVS DDHEGRAAQK RLETLLEERE SKAEKVLQFD PGTKNVTALL MEARDLEARV IILSASEDDA ATVYRAAAML NM TGSGYVW LVGEREISGN ALRYAPDGII GLQLINGKNE SAHISDAVGV VAQAVHELLE KENITDPPRG CVGNTNIWKT GPL FKRVLM SSKYADGVTG RVEFNEDGDR KFANYSIMNL QNRKLVQVGI YNGTHVIPND RKIIWPGGET EKPRGYQMST RLKI VTIHQ EPFVYVKPTM SDGTCKEEFT VNGDPVKKVI CTGPNDTSPG SPRHTVPQCC YGFCVDLLIK LARTMNFTYE VHLVA DGKF GTQERVNNSN KKEWNGMMGE LLSGQADMIV APLTINNERA QYIEFSKPFK YQGLTILVKK EIPRSTLDSF MQPFQS TLW LLVGLSVHVV AVMLYLLDRF SPFGRFKVNS EEEEEDALTL SSAMWFSWGV LLNSGIGEGA PRSFSARILG MVWAGFA MI IVASYTANLA AFLVLDRPEE RITGINDPRL RNPSDKFIYA TVKQSSVDIY FRRQVELSTM YRHMEKHNYE SAAEAIQA V RDNKLHAFIW DSAVLEFEAS QKCDLVTTGE LFFRSGFGIG MRKDSPWKQN VSLSILKSHE NGFMEDLDKT WVRYQECDS RSNAPATLTF ENMAGVFMLV AGGIVAGIFL IFIEIAYKRH KDARRKQMQL AFAAVNVWRK NLQDRKSGRA EPDPKKKATF RAITSTLAS SFKRRRSSKD TSTGGGRGAL QNQKDTVLPR RAIEREEGQL QLCSRHRES

UniProtKB: Glutamate receptor ionotropic, NMDA 1

-
Macromolecule #4: Glutamate receptor ionotropic, NMDA 2B

MacromoleculeName: Glutamate receptor ionotropic, NMDA 2B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 166.162062 KDa
SequenceString: MKPSAECCSP KFWLVLAVLA VSGSKARSQK SAPSIGIAVI LVGTSDEVAI KDAHEKDDFH HLSVVPRVEL VAMNETDPKS IITRICDLM SDRKIQGVVL ADDTDQEAIA QILDFISAQT LTPILGIHGG SSMIMADKDE SSMFFQFGPS IEQQASVMLN I MEEYDWYI ...String:
MKPSAECCSP KFWLVLAVLA VSGSKARSQK SAPSIGIAVI LVGTSDEVAI KDAHEKDDFH HLSVVPRVEL VAMNETDPKS IITRICDLM SDRKIQGVVL ADDTDQEAIA QILDFISAQT LTPILGIHGG SSMIMADKDE SSMFFQFGPS IEQQASVMLN I MEEYDWYI FSIVTTYFPG YQDFVNKIRS TIENSFVGWE LEEVLLLDMS LDDGDSKIQN QLKKLQSPII LLYCTKEEAT YI FEVANSV GLTGYGYTWI VPSLVAGDTD TVPSEFPTGL ISVSYDEWDY GLPARVRDGI AIITTAASDM LSEHSFIPEP KSS CYNTHE KRIYQSNMLN RYLINVTFEG RNLSFSEDGY QMHPKLVIIL LNKERKWERV GKWKDKSLQM KYYVWPRMCP ETEE QEDDH LSIVTLEEAP FVIVESVDPL SGTCMRNTVP CQKRIISENK TDEEPGYIKK CCKGFCIDIL KKISKSVKFT YDLYL VTNG KHGKKINGTW NGMIGEVVMK RAYMAVGSLT INEERSEVVD FSVPFIETGI SVMVSRSNGT VSPSAFLEPF SADVWV MMF VMLLIVSAVA VFVFEYFSPV GYNRCLADGR EPGGPSFTIG KAIWLLWGLV FNNSVPVQNP KGTTSKIMVS VWAFFAV IF LASYTANLAA FMIQEEYVDQ VSGLSDKKFQ RPNDFSPPFR FGTVPNGSTE RNIRNNYAEM HAYMGKFNQR GVDDALLS L KTGKLDAFIY DAAVLNYMAG RDEGCKLVTI GSGKVFASTG YGIAIQKDSG WKRQVDLAIL QLFGDGEMEE LEALWLTGI CHNEKNEVMS SQLDIDNMAG VFYMLGAAMA LSLITFICEH LFYWQFRHCF MGVCSGKPGM VFSISRGIYS CIHGVAIEER QSVMNSPTA TMNNTHSNIL RLLRTAKNMA NLSGVNGSPQ SALDFIRRES SVYDISEHRR SFTHSDCKSY NNPPCEENLF S DYISEVER TFGNLQLKDS NVYQDHYHHH HRPHSIGSTS SIDGLYDCDN PPFTTQPRSI SKKPLDIGLP SSKHSQLSDL YG KFSFKSD RYSGHDDLIR SDVSDISTHT VTYGNIEGNA AKRRKQQYKD SLKKRPASAK SRREFDEIEL AYRRRPPRSP DHK RYFRDK EGLRDFYLDQ FRTKENSPHW EHVDLTDIYK ERSDDFKRDS VSGGGPCTNR SHLKHGTGDK HGVVGGVPAP WEKN LTNVD WEDRSGGNFC RSCPSKLHNY SSTVAGQNSG RQACIRCEAC KKAGNLYDIS EDNSLQELDQ PAAPVAVSSN ASTTK YPQS PTNSKAQKKN RNKLRRQHSY DTFVDLQKEE AALAPRSVSL KDKGRFMDGS PYAHMFEMPA GESSFANKSS VTTAGH HHN NPGSGYMLSK SLYPDRVTQN PFIPTFGDDQ CLLHGSKSYF FRQPTVAGAS KTRPDFRALV TNKPVVSALH GAVPGRF QK DICIGNQSNP CVPNNKNPRA FNGSSNGHVY EKLSSIESDV

UniProtKB: Glutamate receptor ionotropic, NMDA 2B

-
Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.05 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 290 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 9851 / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model from 2D class average
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Number images used: 163121
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
FSC plot (resolution estimation)

+
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