[English] 日本語
Yorodumi
- EMDB-53004: Structure of eIF2B decamer bound to (P)eIF2 alpha and Compound A-(S) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53004
TitleStructure of eIF2B decamer bound to (P)eIF2 alpha and Compound A-(S)
Map data
Sample
  • Complex: Complex of eIF2B decamer bound to (P)eIF2 alpha and Compound A-(S)
    • Protein or peptide: Translation initiation factor eIF2B subunit alpha
    • Protein or peptide: Translation initiation factor eIF2B subunit beta
    • Protein or peptide: Translation initiation factor eIF-2B subunit gamma
    • Protein or peptide: Translation initiation factor eIF-2B subunit delta
    • Protein or peptide: Translation initiation factor eIF2B subunit epsilon
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 1
  • Ligand: ~{N}-[(1~{S})-7-[3-[[ethanoyl(methyl)amino]methyl]phenyl]-5-(trifluoromethyl)-1,2,3,4-tetrahydronaphthalen-1-yl]-2-[[(3~{R},4~{S})-3-fluoranylpiperidin-4-yl]methoxy]-~{N}-methyl-ethanamide
Keywordsintegrated stress response / complex / translation initiation / guanine exchange factor / TRANSLATION
Function / homology
Function and homology information


translation initiation ternary complex / regulation of translation in response to endoplasmic reticulum stress / glial limiting end-foot / HRI-mediated signaling / eukaryotic translation initiation factor 2B complex / response to manganese-induced endoplasmic reticulum stress / Cellular response to mitochondrial stress / positive regulation of type B pancreatic cell apoptotic process / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP ...translation initiation ternary complex / regulation of translation in response to endoplasmic reticulum stress / glial limiting end-foot / HRI-mediated signaling / eukaryotic translation initiation factor 2B complex / response to manganese-induced endoplasmic reticulum stress / Cellular response to mitochondrial stress / positive regulation of type B pancreatic cell apoptotic process / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP / negative regulation of translational initiation in response to stress / PERK-mediated unfolded protein response / PERK regulates gene expression / response to kainic acid / eukaryotic translation initiation factor 2 complex / regulation of translational initiation in response to stress / astrocyte development / astrocyte differentiation / eukaryotic 48S preinitiation complex / oligodendrocyte development / regulation of translational initiation / cytoplasmic translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / positive regulation of translational initiation / Response of EIF2AK4 (GCN2) to amino acid deficiency / response to glucose / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / ovarian follicle development / mitophagy / myelination / translation initiation factor binding / translation initiation factor activity / guanyl-nucleotide exchange factor activity / response to endoplasmic reticulum stress / cellular response to amino acid starvation / stress granule assembly / central nervous system development / hippocampus development / translational initiation / PKR-mediated signaling / response to peptide hormone / ABC-family protein mediated transport / cytoplasmic stress granule / cellular response to UV / regulation of translation / T cell receptor signaling pathway / cellular response to heat / response to heat / ribosome binding / cellular response to oxidative stress / positive regulation of apoptotic process / synapse / GTP binding / mitochondrion / RNA binding / extracellular exosome / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Translation initiation factor eIF-2B subunit alpha, N-terminal / Translation initiation factor eIF-2B subunit epsilon, N-terminal / Translation initiation factor eIF-2B subunit epsilon, W2 domain / : / : / : / : / : / EIF2B subunit epsilon LbH domain / Initiation factor 2B-related ...Translation initiation factor eIF-2B subunit alpha, N-terminal / Translation initiation factor eIF-2B subunit epsilon, N-terminal / Translation initiation factor eIF-2B subunit epsilon, W2 domain / : / : / : / : / : / EIF2B subunit epsilon LbH domain / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Initiation factor 2 subunit family / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / IF2a, S1-like domain / Eukaryotic translation initiation factor 2 alpha subunit / Nucleotidyl transferase domain / Nucleotidyl transferase / NagB/RpiA transferase-like / Trimeric LpxA-like superfamily / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Nucleotide-diphospho-sugar transferases / S1 domain / Armadillo-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Eukaryotic translation initiation factor 2 subunit 1 / Translation initiation factor eIF2B subunit beta / Translation initiation factor eIF2B subunit epsilon / Translation initiation factor eIF2B subunit alpha / Translation initiation factor eIF2B subunit gamma / Translation initiation factor eIF2B subunit delta
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsShilliday F / Maia de Oliveira T / Gancedo-Rodrigo M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2026
Title: A molecular stabiliser of an inhibitory eIF2B-eIF2(αP) complex activates the Integrated Stress Response.
Authors: Fiona Shilliday / Miguel Gancedo-Rodrigo / Ginto George / Shintaro Aibara / Santosh Adhikari / Syedah Neha Ashraf / Evelyne J Barrey / Paolo A Centrella / Damian Crowther / Paige Dickson / ...Authors: Fiona Shilliday / Miguel Gancedo-Rodrigo / Ginto George / Shintaro Aibara / Santosh Adhikari / Syedah Neha Ashraf / Evelyne J Barrey / Paolo A Centrella / Damian Crowther / Paige Dickson / Diana Gikunju / Marie-Aude Guié / John P Guilinger / Anders Gunnarsson / Heather P Harding / Christopher D Hupp / Rachael Jetson / Anthony D Keefe / JeeSoo Monica Kim / Richard J Lewis / Taiana Maia de Oliveira / Jennifer Le-Marshall / Usha Narayanan / Katherine A Nugai / Dušan Petrović / Emma Rivers / David Ron / Daisy Stringfellow / Karl Syson / Lewis Ward / John T S Yeoman / Yan Yu / Ying Zhang / Alisa Zyryanova / David J Baker / Perla Breccia / John E Linley /
Abstract: Eukaryotic initiation factor 2B (eIF2B), a guanine nucleotide exchange factor (GEF), promotes protein synthesis by charging translation initiation factor 2 (eIF2) with GTP. Stress-induced ...Eukaryotic initiation factor 2B (eIF2B), a guanine nucleotide exchange factor (GEF), promotes protein synthesis by charging translation initiation factor 2 (eIF2) with GTP. Stress-induced phosphorylation of eIF2 on its α-subunit [eIF2(αP)] inhibits this reaction triggering a protective Integrated Stress Response (ISR). A DNA-encoded chemical library (DEL) screen for modulators of eIF2B, led to the identification of a chemical series that stabilises the inactive state of eIF2B, stimulating the ISR. Cryo-EM of compound-bound eIF2B reveals a conformational switch to the inactive state engaged by eIF2(αP). In cells, compound activity is sensitive to eIF2's phosphorylation state and to a competing eIF2B ligand (ISRIB) that activates the GEF allosterically. These findings establish the feasibility of targeting eIF2B with a drug-like allosteric inhibitor, that serves as an ISR activator (ISRAC), paving the way to explore the therapeutic potential of eIF2B-directed ISR activation.
History
DepositionMar 4, 2025-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53004.png

Downloads & links

-
Map

FileDownload / File: emd_53004.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 380 pix.
= 324.9 Å		0.86 Å/pix.
x 380 pix.
= 324.9 Å		0.86 Å/pix.
x 380 pix.
= 324.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.2809643 - 0.48123908
Average (Standard dev.)-0.0001338514 (±0.01745821)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 324.9 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_53004_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_53004_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_53004_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of eIF2B decamer bound to (P)eIF2 alpha and Compound A-(S)

EntireName: Complex of eIF2B decamer bound to (P)eIF2 alpha and Compound A-(S)
Components
  • Complex: Complex of eIF2B decamer bound to (P)eIF2 alpha and Compound A-(S)
    • Protein or peptide: Translation initiation factor eIF2B subunit alpha
    • Protein or peptide: Translation initiation factor eIF2B subunit beta
    • Protein or peptide: Translation initiation factor eIF-2B subunit gamma
    • Protein or peptide: Translation initiation factor eIF-2B subunit delta
    • Protein or peptide: Translation initiation factor eIF2B subunit epsilon
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 1
  • Ligand: ~{N}-[(1~{S})-7-[3-[[ethanoyl(methyl)amino]methyl]phenyl]-5-(trifluoromethyl)-1,2,3,4-tetrahydronaphthalen-1-yl]-2-[[(3~{R},4~{S})-3-fluoranylpiperidin-4-yl]methoxy]-~{N}-methyl-ethanamide

-
Supramolecule #1: Complex of eIF2B decamer bound to (P)eIF2 alpha and Compound A-(S)

SupramoleculeName: Complex of eIF2B decamer bound to (P)eIF2 alpha and Compound A-(S)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Translation initiation factor eIF2B subunit alpha

MacromoleculeName: Translation initiation factor eIF2B subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.060656 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLEVLFQG PMDDKELIEY FKSQMKEDPD MASAVAAIRT LLEFLKRDKG ETIQGLRANL TSAIETLCGV DSSVAVSSG GELFLRFISL ASLEYSDYSK CKKIMIERGE LFLRRISLSR NKIADLCHTF IKDGATILTH AYSRVVLRVL E AAVAAKKR ...String:
MGSSHHHHHH SSGLEVLFQG PMDDKELIEY FKSQMKEDPD MASAVAAIRT LLEFLKRDKG ETIQGLRANL TSAIETLCGV DSSVAVSSG GELFLRFISL ASLEYSDYSK CKKIMIERGE LFLRRISLSR NKIADLCHTF IKDGATILTH AYSRVVLRVL E AAVAAKKR FSVYVTESQP DLSGKKMAKA LCHLNVPVTV VLDAAVGYIM EKADLVIVGA EGVVENGGII NKIGTNQMAV CA KAQNKPF YVVAESFKFV RLFPLNQQDV PDKFKYKADT LKVAQTGQDL KEEHPWVDYT APSLITLLFT DLGVLTPSAV SDE LIKLYL

UniProtKB: Translation initiation factor eIF2B subunit alpha

-
Macromolecule #2: Translation initiation factor eIF2B subunit beta

MacromoleculeName: Translation initiation factor eIF2B subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.039547 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPGSAAKGSE LSERIESFVE TLKRGGGPRS SEEMARETLG LLRQIITDHR WSNAGELMEL IRREGRRMTA AQPSETTVGN MVRRVLKII REEYGRLHGR SDESDQQESL HKLLTSGGLN EDFSFHYAQL QSNIIEAINE LLVELEGTME NIAAQALEHI H SNEVIMTI ...String:
MPGSAAKGSE LSERIESFVE TLKRGGGPRS SEEMARETLG LLRQIITDHR WSNAGELMEL IRREGRRMTA AQPSETTVGN MVRRVLKII REEYGRLHGR SDESDQQESL HKLLTSGGLN EDFSFHYAQL QSNIIEAINE LLVELEGTME NIAAQALEHI H SNEVIMTI GFSRTVEAFL KEAARKRKFH VIVAECAPFC QGHEMAVNLS KAGIETTVMT DAAIFAVMSR VNKVIIGTKT IL ANGALRA VTGTHTLALA AKHHSTPLIV CAPMFKLSPQ FPNEEDSFHK FVAPEEVLPF TEGDILEKVS VHCPVFDYVP PEL ITLFIS NIGGNAPSYI YRLMSELYHP DDHVL

UniProtKB: Translation initiation factor eIF2B subunit beta

-
Macromolecule #3: Translation initiation factor eIF-2B subunit gamma

MacromoleculeName: Translation initiation factor eIF-2B subunit gamma / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.30423 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEFQAVVMAV GGGSRMTDLT SSIPKPLLPV GNKPLIWYPL NLLERVGFEE VIVVTTRDVQ KALCAEFKMK MKPDIVCIPD DADMGTADS LRYIYPKLKT DVLVLSCDLI TDVALHEVVD LFRAYDASLA MLMRKGQDSI EPVPGQKGKK KAVEQRDFIG V DSTGKRLL ...String:
MEFQAVVMAV GGGSRMTDLT SSIPKPLLPV GNKPLIWYPL NLLERVGFEE VIVVTTRDVQ KALCAEFKMK MKPDIVCIPD DADMGTADS LRYIYPKLKT DVLVLSCDLI TDVALHEVVD LFRAYDASLA MLMRKGQDSI EPVPGQKGKK KAVEQRDFIG V DSTGKRLL FMANEADLDE ELVIKGSILQ KHPRIRFHTG LVDAHLYCLK KYIVDFLMEN GSITSIRSEL IPYLVRKQFS SA SSQQGQE EKEEDLKKKE LKSLDIYSFI KEANTLNLAP YDACWNACRG DRWEDLSRSQ VRCYVHIMKE GLCSRVSTLG LYM EANRQV PKLLSALCPE EPPVHSSAQI VSKHLVGVDS LIGPETQIGE KSSIKRSVIG SSCLIKDRVT ITNCLLMNSV TVEE GSNIQ GSVICNNAVI EKGADIKDCL IGSGQRIEAK AKRVNEVIVG NDQLMEI

UniProtKB: Translation initiation factor eIF2B subunit gamma

-
Macromolecule #4: Translation initiation factor eIF-2B subunit delta

MacromoleculeName: Translation initiation factor eIF-2B subunit delta / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.640168 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAVAVAVRE DSGSGMKAEL PPGPGAVGRE MTKEEKLQLR KEKKQQKKKR KEEKGAEPET GSAVSAAQCQ VGPTRELPES GIQLGTPRE KVPAGRSKAE LRAERRAKQE AERALKQARK GEQGGPPPKA SPSTAGETPS GVKRLPEYPQ VDDLLLRRLV K KPERQQVP ...String:
MAAVAVAVRE DSGSGMKAEL PPGPGAVGRE MTKEEKLQLR KEKKQQKKKR KEEKGAEPET GSAVSAAQCQ VGPTRELPES GIQLGTPRE KVPAGRSKAE LRAERRAKQE AERALKQARK GEQGGPPPKA SPSTAGETPS GVKRLPEYPQ VDDLLLRRLV K KPERQQVP TRKDYGSKVS LFSHLPQYSR QNSLTQFMSI PSSVIHPAMV RLGLQYSQGL VSGSNARCIA LLRALQQVIQ DY TTPPNEE LSRDLVNKLK PYMSFLTQCR PLSASMHNAI KFLNKEITSV GSSKREEEAK SELRAAIDRY VQEKIVLAAQ AIS RFAYQK ISNGDVILVY GCSSLVSRIL QEAWTEGRRF RVVVVDSRPW LEGRHTLRSL VHAGVPASYL LIPAASYVLP EVSK VLLGA HALLANGSVM SRVGTAQLAL VARAHNVPVL VCCETYKFCE RVQTDAFVSN ELDDPDDLQC KRGEHVALAN WQNHA SLRL LNLVYDVTPP ELVDLVITEL GMIPCSSVPV VLRVKSSDQ

UniProtKB: Translation initiation factor eIF2B subunit delta

-
Macromolecule #5: Translation initiation factor eIF2B subunit epsilon

MacromoleculeName: Translation initiation factor eIF2B subunit epsilon / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.773133 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLEVLFQG PMAAPVVAPP GVVVSRANKR SGAGPGGSGG GGARGAEEEP PPPLQAVLVA DSFDRRFFPI SKDQPRVLL PLANVALIDY TLEFLTATGV QETFVFCCWK AAQIKEHLLK SKWCRPTSLN VVRIITSELY RSLGDVLRDV D AKALVRSD ...String:
MGSSHHHHHH SSGLEVLFQG PMAAPVVAPP GVVVSRANKR SGAGPGGSGG GGARGAEEEP PPPLQAVLVA DSFDRRFFPI SKDQPRVLL PLANVALIDY TLEFLTATGV QETFVFCCWK AAQIKEHLLK SKWCRPTSLN VVRIITSELY RSLGDVLRDV D AKALVRSD FLLVYGDVIS NINITRALEE HRLRRKLEKN VSVMTMIFKE SSPSHPTRCH EDNVVVAVDS TTNRVLHFQK TQ GLRRFAF PLSLFQGSSD GVEVRYDLLD CHISICSPQV AQLFTDNFDY QTRDDFVRGL LVNEEILGNQ IHMHVTAKEY GAR VSNLHM YSAVCADVIR RWVYPLTPEA NFTDSTTQSC THSRHNIYRG PEVSLGHGSI LEENVLLGSG TVIGSNCFIT NSVI GPGCH IGDNVVLDQT YLWQGVRVAA GAQIHQSLLC DNAEVKERVT LKPRSVLTSQ VVVGPNITLP EGSVISLHPP DAEED EDDG EFSDDSGADQ EKDKVKMKGY NPAEVGAAGK GYLWKAAGMN MEEEEELQQN LWGLKINMEE ESESESEQSM DSEEPD SRG GSPQMDDIKV FQNEVLGTLQ RGKEENISCD NLVLEINSLK YAYNISLKEV MQVLSHVVLE FPLQQMDSPL DSSRYCA LL LPLLKAWSPV FRNYIKRAAD HLEALAAIED FFLEHEALGI SMAKVLMAFY QLEILAEETI LSWFSQRDTT DKGQQLRK N QQLQRFIQWL KEAEEESSED D

UniProtKB: Translation initiation factor eIF2B subunit epsilon

-
Macromolecule #6: Eukaryotic translation initiation factor 2 subunit 1

MacromoleculeName: Eukaryotic translation initiation factor 2 subunit 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.530879 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSMPGLSCRF YQHKFPEVED VVMVNVRSIA EMGAYVSLLE YNNIEGMILL SEL(SEP)RRRIRS INKLIRIGRN ECVVVI RVD KEKGYIDLSK RRVSPEEAIK CEDKFTKSKT VYSILRHVAE VLEYTKDEQL ESLFQRTAWV FDDKYKRPGY GAYDAFK HA VSDPSILDSL ...String:
GSMPGLSCRF YQHKFPEVED VVMVNVRSIA EMGAYVSLLE YNNIEGMILL SEL(SEP)RRRIRS INKLIRIGRN ECVVVI RVD KEKGYIDLSK RRVSPEEAIK CEDKFTKSKT VYSILRHVAE VLEYTKDEQL ESLFQRTAWV FDDKYKRPGY GAYDAFK HA VSDPSILDSL DLNEDEREVL INNINRRLTP QLERAPGGLN DIFEAQKIEW HE

UniProtKB: Eukaryotic translation initiation factor 2 subunit 1

-
Macromolecule #7: ~{N}-[(1~{S})-7-[3-[[ethanoyl(methyl)amino]methyl]phenyl]-5-(trif...

MacromoleculeName: ~{N}-[(1~{S})-7-[3-[[ethanoyl(methyl)amino]methyl]phenyl]-5-(trifluoromethyl)-1,2,3,4-tetrahydronaphthalen-1-yl]-2-[[(3~{R},4~{S})-3-fluoranylpiperidin-4-yl]methoxy]-~{N}-methyl-ethanamide
type: ligand / ID: 7 / Number of copies: 1 / Formula: A1I5O
Molecular weightTheoretical: 563.627 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 60.0 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: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 18192
Initial angle assignmentType: MAXIMUM LIKELIHOOD
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