[English] 日本語
Yorodumi
- EMDB-46530: Gly-,Glu-,(S)-DQP-997-74 bound GluN1a-2B-2D NMDAR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-46530
TitleGly-,Glu-,(S)-DQP-997-74 bound GluN1a-2B-2D NMDAR
Map dataComposite map
Sample
  • Complex: tri-heteromeric GluN1-2B-2D NMDAR
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2D
  • Ligand: GLYCINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: GLUTAMIC ACID
  • Ligand: 4-{(3R,5S)-5-(4-chlorophenyl)-3-[4-(4-chlorophenyl)-2-oxo-1,2-dihydroquinolin-3-yl]pyrazolidin-1-yl}-3,3-difluoro-4-oxobutanoic acid
KeywordsN-methyl-D-aspartate receptor / (S)-DQP-997-74 / GluN2B / GluN2D / MEMBRANE PROTEIN
Function / homology
Function and homology information


glycine-gated cation channel activity / regulation of sensory perception of pain / excitatory chemical synaptic transmission / Activated NTRK2 signals through FYN / Synaptic adhesion-like molecules / cellular response to L-glutamate / response to glycine / propylene metabolic process / negative regulation of dendritic spine maintenance / regulation of monoatomic cation transmembrane transport ...glycine-gated cation channel activity / regulation of sensory perception of pain / excitatory chemical synaptic transmission / Activated NTRK2 signals through FYN / Synaptic adhesion-like molecules / cellular response to L-glutamate / response to glycine / propylene metabolic process / negative regulation of dendritic spine maintenance / regulation of monoatomic cation transmembrane transport / Assembly and cell surface presentation of NMDA receptors / NMDA glutamate receptor activity / voltage-gated monoatomic cation channel activity / Neurexins and neuroligins / neurotransmitter receptor complex / NMDA selective glutamate receptor complex / ligand-gated sodium channel activity / calcium ion transmembrane import into cytosol / glutamate receptor signaling pathway / glutamate binding / protein heterotetramerization / glycine binding / positive regulation of reactive oxygen species biosynthetic process / positive regulation of calcium ion transport into cytosol / Negative regulation of NMDA receptor-mediated neuronal transmission / startle response / Unblocking of NMDA receptors, glutamate binding and activation / monoatomic cation transmembrane transport / regulation of neuronal synaptic plasticity / Long-term potentiation / monoatomic cation transport / excitatory synapse / positive regulation of excitatory postsynaptic potential / monoatomic ion channel complex / synaptic cleft / glutamate-gated receptor activity / calcium ion homeostasis / MECP2 regulates neuronal receptors and channels / presynaptic active zone membrane / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / EPHB-mediated forward signaling / sodium ion transmembrane transport / Ras activation upon Ca2+ influx through NMDA receptor / ionotropic glutamate receptor signaling pathway / positive regulation of synaptic transmission, glutamatergic / hippocampal mossy fiber to CA3 synapse / adult locomotory behavior / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / synaptic membrane / postsynaptic density membrane / terminal bouton / brain development / visual learning / calcium ion transmembrane transport / regulation of synaptic plasticity / long-term synaptic potentiation / late endosome / synaptic vesicle / signaling receptor activity / amyloid-beta binding / RAF/MAP kinase cascade / chemical synaptic transmission / dendritic spine / response to ethanol / postsynaptic membrane / cytoskeleton / learning or memory / lysosome / calmodulin binding / neuron projection / postsynaptic density / synapse / dendrite / calcium ion binding / endoplasmic reticulum membrane / protein-containing complex binding / glutamatergic synapse / 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 2D / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.71 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: Neuron / Year: 2025
Title: Structural basis for channel gating and blockade in tri-heteromeric GluN1-2B-2D NMDA receptor.
Authors: Hyunook Kang / Max Epstein / Tue G Banke / Riley Perszyk / Noriko Simorowski / Srinu Paladugu / Dennis C Liotta / Stephen F Traynelis / Hiro Furukawa /
Abstract: Discrete activation of N-methyl-D-aspartate receptor (NMDAR) subtypes by glutamate and the co-agonist glycine is fundamental to neuroplasticity. A distinct variant, the tri-heteromeric receptor, ...Discrete activation of N-methyl-D-aspartate receptor (NMDAR) subtypes by glutamate and the co-agonist glycine is fundamental to neuroplasticity. A distinct variant, the tri-heteromeric receptor, comprising glycine-binding GluN1 and two types of glutamate-binding GluN2 subunits, exhibits unique pharmacological characteristics, notably enhanced sensitivity to the anti-depressant channel blocker S-(+)-ketamine. Despite its significance, the structural mechanisms underlying ligand gating and channel blockade of tri-heteromeric NMDARs remain poorly understood. Here, we identify and characterize tri-heteromeric GluN1-2B-2D NMDAR in the adult brain, resolving its structures in the activated, inhibited, and S-(+)-ketamine-blocked states. These structures reveal the ligand-dependent conformational dynamics that modulate the tension between the extracellular domain and transmembrane channels, governing channel gating and blockade. Additionally, we demonstrate that the inhibitor (S)-DQP-997-74 selectively decouples linker tension in GluN2D, offering insights into subtype-selective targeting for cognitive modulation.
History
DepositionAug 9, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_46530.png

Downloads & links

-
Map

FileDownload / File: emd_46530.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 400 pix.
= 344.4 Å		0.86 Å/pix.
x 400 pix.
= 344.4 Å		0.86 Å/pix.
x 400 pix.
= 344.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.861 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.27892232 - 1.9991016
Average (Standard dev.)0.009653019 (±0.04287998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 344.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: TMD local refined map

Fileemd_46530_additional_1.map
AnnotationTMD local refined map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: ECD local refined map

Fileemd_46530_additional_2.map
AnnotationECD local refined map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Consensus map

Fileemd_46530_additional_3.map
AnnotationConsensus map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : tri-heteromeric GluN1-2B-2D NMDAR

EntireName: tri-heteromeric GluN1-2B-2D NMDAR
Components
  • Complex: tri-heteromeric GluN1-2B-2D NMDAR
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2D
  • Ligand: GLYCINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: GLUTAMIC ACID
  • Ligand: 4-{(3R,5S)-5-(4-chlorophenyl)-3-[4-(4-chlorophenyl)-2-oxo-1,2-dihydroquinolin-3-yl]pyrazolidin-1-yl}-3,3-difluoro-4-oxobutanoic acid

-
Supramolecule #1: tri-heteromeric GluN1-2B-2D NMDAR

SupramoleculeName: tri-heteromeric GluN1-2B-2D NMDAR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 377 KDa

-
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: 92.691828 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DPKIVNIGAV LSTRKHEQMF REAVNQANKR HGSWKIQLNA TSVTHKPNAI QMALSVCEDL ISSQVYAILV SHPPTPNDHF TPTPVSYTA GFYRIPVLGL TTRMSIYSDK SIHLSFLRTV PPYSHQSSVW FEMMRVYSWN HIILLVSDDH EGRAAQKRLE T LLEERESK ...String:
DPKIVNIGAV LSTRKHEQMF REAVNQANKR HGSWKIQLNA TSVTHKPNAI QMALSVCEDL ISSQVYAILV SHPPTPNDHF TPTPVSYTA GFYRIPVLGL TTRMSIYSDK SIHLSFLRTV PPYSHQSSVW FEMMRVYSWN HIILLVSDDH EGRAAQKRLE T LLEERESK AEKVLQFDPG TKNVTALLME AKELEARVII LSASEDDAAT VYRAAAMLNM TGSGYVWLVG EREISGNALR YA PDGILGL QLINGKNESA HISDAVGVVA QAVHELLEKE NITDPPRGCV GNTNIWKTGP LFKRVLMSSK YADGVTGRVE FNE DGDRKF ANYSIMNLQN RKLVQVGIYN GTHVIPNDRK IIWPGGETEK PRGYQMSTRL KIVTIHQEPF VYVKPTLSDG TCKE EFTVN GDPVKKVICT GPNDTSPGSP RHTVPQCCYG FCIDLLIKLA RTMNFTYEVH LVADGKFGTQ ERVNNSNKKE WNGMM GELL SGQADMIVAP LTINNERAQY IEFSKPFKYQ GLTILVKKEI PRSTLDSFMQ PFQSTLWLLV GLSVHVVAVM LYLLDR FSP FGRFKVNSEE EEEDALTLSS AMWFSWGVLL NSGIGEGAPR SFSARILGMV WAGFAMIIVA SYTANLAAFL VLDRPEE RI TGINDPRLRN PSDKFIYATV KQSSVDIYFR RQVELSTMYR HMEKHNYESA AEAIQAVRDN KLHAFIWDSA VLEFEASQ K CDLVTTGELF FRSGFGIGMR KDSPWKQNVS LSILKSHENG FMEDLDKTWV RYQECDSRSN APATLTFENM AGVFMLVAG GIVAGIFLIF IEIAYKRHKD ANGAQ

UniProtKB: Glutamate receptor ionotropic, NMDA 1

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

MacromoleculeName: Glutamate receptor ionotropic, NMDA 2B / type: protein_or_peptide / ID: 2
Details: Twin-Strep tag (WSHPQFEKGGGSGGGSGGSAWSHPQFEKGALVPRG) C-terminal p2A tag (GSGATNFSLLKQAGDVEENPG)
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 98.622172 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 GGPGSGATNF SLLKQAGDVE ENPG

UniProtKB: Glutamate receptor ionotropic, NMDA 2B

-
Macromolecule #3: Glutamate receptor ionotropic, NMDA 2D

MacromoleculeName: Glutamate receptor ionotropic, NMDA 2D / type: protein_or_peptide / ID: 3 / Details: 1D4-tag (TETSQVAPA) / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 94.120609 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: FPEEAPGPGG AGGPGGGLGG ARPLNVALVF SGPAYAAEAA RLGPAVAAAV RSPGLDVRPV ALVLNGSDPR SLVLQLCDLL SGLRVHGVV FEDDSRAPAV APILDFLSAQ TSLPIVAVHG GAALVLTPKE KGSTFLQLGS STEQQLQVIF EVLEEYDWTS F VAVTTRAP ...String:
FPEEAPGPGG AGGPGGGLGG ARPLNVALVF SGPAYAAEAA RLGPAVAAAV RSPGLDVRPV ALVLNGSDPR SLVLQLCDLL SGLRVHGVV FEDDSRAPAV APILDFLSAQ TSLPIVAVHG GAALVLTPKE KGSTFLQLGS STEQQLQVIF EVLEEYDWTS F VAVTTRAP GHRAFLSYIE VLTDGSLVGW EHRGALTLDP GAGEAVLSAQ LRSVSAQIRL LFCAREEAEP VFRAAEEAGL TG SGYVWFM VGPQLAGGGG SGAPGEPPLL PGGAPLPAGL FAVRSAGWRD DLARRVAAGV AVVARGAQAL LRDYGFLPEL GHD CRAQNR THRGESLHRY FMNITWDNRD YSFNEDGFLV NPSLVVISLT RDRTWEVVGS WEQQTLRLKY PLWSRYGRFL QPVD DTQHL TVATLEERPF VIVEPADPIS GTCIRDSVPC RSQLNRTHSP PPDAPRPEKR CCKGFCIDIL KRLAHTIGFS YDLYL VTNG KHGKKIDGVW NGMIGEVFYQ RADMAIGSLT INEERSEIVD FSVPFVETGI SVMVARSNGT VSPSAFLEPY SPAVWV MMF VMCLTVVAVT VFIFEYLSPV GYNRSLATGK RPGGSTFTIG KSIWLLWALV FNNSVPVENP RGTTSKIMVL VWAFFAV IF LASYTANLAA FMIQEEYVDT VSGLSDRKFQ RPQEQYPPLK FGTVPNGSTE KNIRSNYPDM HSYMVRYNQP RVEEALTQ L KAGKLDAFIY DAAVLNYMAR KDEGCKLVTI GSGKVFATTG YGIALHKGSR WKRPIDLALL QFLGDDEIEM LERLWLSGI CHNDKIEVMS SKLDIDNMAG VFYMLLVAMG LSLLVFAWEH LVYWRLRHCL GPTETSQVAP A

UniProtKB: Glutamate receptor ionotropic, NMDA 2D

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Macromolecule #7: GLUTAMIC ACID

MacromoleculeName: GLUTAMIC ACID / type: ligand / ID: 7 / Number of copies: 2 / Formula: GLU
Molecular weightTheoretical: 147.129 Da
Chemical component information

ChemComp-GLU:
GLUTAMIC ACID

-
Macromolecule #8: 4-{(3R,5S)-5-(4-chlorophenyl)-3-[4-(4-chlorophenyl)-2-oxo-1,2-dih...

MacromoleculeName: 4-{(3R,5S)-5-(4-chlorophenyl)-3-[4-(4-chlorophenyl)-2-oxo-1,2-dihydroquinolin-3-yl]pyrazolidin-1-yl}-3,3-difluoro-4-oxobutanoic acid
type: ligand / ID: 8 / Number of copies: 1 / Formula: A1A15
Molecular weightTheoretical: 572.387 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN 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: 61.0 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

+
Image processing

Particle selectionNumber selected: 1317548
Startup modelType of model: OTHER / Details: Ab initio reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 100870
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
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

8e96

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

PDB-9d3b:
Gly-,Glu-,(S)-DQP-997-74 bound GluN1a-2B-2D NMDAR

+
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