[English] 日本語
Yorodumi
- EMDB-15829: CRL4CSA-E2-Ub (state 2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15829
TitleCRL4CSA-E2-Ub (state 2)
Map dataThe main map.
Sample
  • Complex: C(N)RL4CSA-E2-Ub complex.
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 D2
    • Protein or peptide: NEDD8
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: Ubiquitin
    • Protein or peptide: DNA excision repair protein ERCC-8
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Cullin-4A
  • Ligand: ZINC ION
KeywordsDNA repair / transcription / ubiqutin / cryo-EM
Function / homology
Function and homology information


regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / response to auditory stimulus / cellular response to camptothecin / negative regulation of beige fat cell differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / negative regulation of mitophagy / (E3-independent) E2 ubiquitin-conjugating enzyme / cullin-RING ubiquitin ligase complex ...regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / response to auditory stimulus / cellular response to camptothecin / negative regulation of beige fat cell differentiation / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / negative regulation of mitophagy / (E3-independent) E2 ubiquitin-conjugating enzyme / cullin-RING ubiquitin ligase complex / regulation of xenophagy / double-strand break repair via classical nonhomologous end joining / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / cellular response to chemical stress / Cul7-RING ubiquitin ligase complex / single strand break repair / regulation of cell cycle process / neural crest cell differentiation / RNA polymerase II transcription initiation surveillance / positive regulation by virus of viral protein levels in host cell / positive regulation of protein autoubiquitination / protein neddylation / spindle assembly involved in female meiosis / regulation of BMP signaling pathway / NEDD8 ligase activity / epigenetic programming in the zygotic pronuclei / regulation of mitophagy / negative regulation of response to oxidative stress / regulation of centrosome duplication / protein K27-linked ubiquitination / UV-damage excision repair / VCB complex / Cul5-RING ubiquitin ligase complex / E2 ubiquitin-conjugating enzyme / regulation of TOR signaling / ubiquitin-ubiquitin ligase activity / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / biological process involved in interaction with symbiont / negative regulation of DNA-templated DNA replication / regulation of mitotic cytokinesis / Cul3-RING ubiquitin ligase complex / regulation of DNA damage checkpoint / regulation of mitotic cell cycle phase transition / negative regulation of type I interferon production / regulation of miRNA-mediated gene silencing / regulation of natural killer cell activation / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / WD40-repeat domain binding / Prolactin receptor signaling / regulation of cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / regulation of stem cell population maintenance / Cul4B-RING E3 ubiquitin ligase complex / TGF-beta receptor signaling activates SMADs / ubiquitin ligase complex scaffold activity / response to UV / ubiquitin conjugating enzyme activity / negative regulation of adipose tissue development / regulation of proteolysis / regulation of cellular response to stress / limb development / regulation of postsynapse assembly / viral release from host cell / protein monoubiquitination / anatomical structure morphogenesis / cullin family protein binding / centrosome duplication / regulation of DNA-templated DNA replication initiation / positive regulation of viral genome replication / positive regulation of gluconeogenesis / cilium assembly / protein autoubiquitination / ubiquitin-like ligase-substrate adaptor activity / intrinsic apoptotic signaling pathway / ribosome-associated ubiquitin-dependent protein catabolic process / signal transduction in response to DNA damage / negative regulation of insulin receptor signaling pathway / Nuclear events stimulated by ALK signaling in cancer / protein K48-linked ubiquitination / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / in utero embryonic development / Maturation of protein E / Maturation of protein E / transcription-coupled nucleotide-excision repair / post-translational protein modification / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / cellular response to amino acid stimulus / Endosomal Sorting Complex Required For Transport (ESCRT)
Similarity search - Function
DNA excision repair protein Rad28/ERCC8/Ckn1/ATCSA-1 / Nedd8-like ubiquitin / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / : / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin, N-terminal / Cullin repeat-like-containing domain superfamily ...DNA excision repair protein Rad28/ERCC8/Ckn1/ATCSA-1 / Nedd8-like ubiquitin / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / : / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin, N-terminal / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin alpha solenoid domain / Cullin / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / Cullin family profile. / : / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / WD domain, G-beta repeat / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 D2 / E3 ubiquitin-protein ligase RBX1 / DNA excision repair protein ERCC-8 / Cullin-4A / Ubiquitin-like protein NEDD8 / DNA damage-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKokic G / Cramer P
Funding support Germany, European Union, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2067/1-390729940 Germany
European Research Council (ERC)Advanced Investigator Grant CHROMATRANS (grant agreement No. 882357)European Union
CitationJournal: To Be Published
Title: C(N)RL4CSA-E2-Ub (state 2)
Authors: Kokic G / Cramer P
History
DepositionSep 16, 2022-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15829.png

Downloads & links

-
Map

FileDownload / File: emd_15829.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe main map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 340 pix.
= 357. Å		1.05 Å/pix.
x 340 pix.
= 357. Å		1.05 Å/pix.
x 340 pix.
= 357. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.26
Minimum - Maximum-2.6552105 - 5.3308387
Average (Standard dev.)-0.00025346928 (±0.13746336)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 356.99997 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map corresponding to the main map.

Fileemd_15829_half_map_1.map
AnnotationHalf map corresponding to the main map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map corresponding to the main map.

Fileemd_15829_half_map_2.map
AnnotationHalf map corresponding to the main map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : C(N)RL4CSA-E2-Ub complex.

EntireName: C(N)RL4CSA-E2-Ub complex.
Components
  • Complex: C(N)RL4CSA-E2-Ub complex.
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 D2
    • Protein or peptide: NEDD8
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: Ubiquitin
    • Protein or peptide: DNA excision repair protein ERCC-8
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: Cullin-4A
  • Ligand: ZINC ION

-
Supramolecule #1: C(N)RL4CSA-E2-Ub complex.

SupramoleculeName: C(N)RL4CSA-E2-Ub complex. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Ubiquitin-conjugating enzyme E2 D2

MacromoleculeName: Ubiquitin-conjugating enzyme E2 D2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.755227 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MALKRIHKEL NDLARDPPAQ CSAGPVGDDM FHWQATIMGP NDSPYQGGVF FLTIHFPTDY PFKPPKVAFT TRIYHPNINS NGSICLDIL RSQWSPALTI SKVLLSICSL LCDPNPDDPL VPEIARIYKT DREKYNRIAR EWTQKYAM

UniProtKB: Ubiquitin-conjugating enzyme E2 D2

-
Macromolecule #2: NEDD8

MacromoleculeName: NEDD8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.573978 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MLIKVKTLTG KEIEIDIEPT DKVERIKERV EEKEGIPPQQ QRLIYSGKQM NDEKTAADYK ILGGSVLHLV LALRGG

UniProtKB: Ubiquitin-like protein NEDD8

-
Macromolecule #3: E3 ubiquitin-protein ligase RBX1

MacromoleculeName: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.289977 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MAAAMDVDTP SGTNSGAGKK RFEVKKWNAV ALWAWDIVVD NCAICRNHIM DLCIECQANQ ASATSEECTV AWGVCNHAFH FHCISRWLK TRQVCPLDNR EWEFQKYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

-
Macromolecule #4: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.576831 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

UniProtKB: Polyubiquitin-C

-
Macromolecule #5: DNA excision repair protein ERCC-8

MacromoleculeName: DNA excision repair protein ERCC-8 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.10716 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MLGFLSARQT GLEDPLRLRR AESTRRVLGL ELNKDRDVER IHGGGINTLD IEPVEGRYML SGGSDGVIVL YDLENSSRQS YYTCKAVCS IGRDHPDVHR YSVETVQWYP HDTGMFTSSS FDKTLKVWDT NTLQTADVFN FEETVYSHHM SPVSTKHCLV A VGTRGPKV ...String:
MLGFLSARQT GLEDPLRLRR AESTRRVLGL ELNKDRDVER IHGGGINTLD IEPVEGRYML SGGSDGVIVL YDLENSSRQS YYTCKAVCS IGRDHPDVHR YSVETVQWYP HDTGMFTSSS FDKTLKVWDT NTLQTADVFN FEETVYSHHM SPVSTKHCLV A VGTRGPKV QLCDLKSGSC SHILQGHRQE ILAVSWSPRY DYILATASAD SRVKLWDVRR ASGCLITLDQ HNGKKSQAVE SA NTAHNGK VNGLCFTSDG LHLLTVGTDN RMRLWNSSNG ENTLVNYGKV CNNSKKGLKF TVSCGCSSEF VFVPYGSTIA VYT VYSGEQ ITMLKGHYKT VDCCVFQSNF QELYSGSRDC NILAWVPSLY EPVPDDDETT TKSQLNPAFE DAWSSSDEEG

UniProtKB: DNA excision repair protein ERCC-8

-
Macromolecule #6: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 127.097469 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACIL EYKQSGESID IITRAHGNVQ DRIGRPSETG IIGIIDPECR MIGLRLYDGL FKVIPLDRDN KELKAFNIRL E ELHVIDVK ...String:
MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACIL EYKQSGESID IITRAHGNVQ DRIGRPSETG IIGIIDPECR MIGLRLYDGL FKVIPLDRDN KELKAFNIRL E ELHVIDVK FLYGCQAPTI CFVYQDPQGR HVKTYEVSLR EKEFNKGPWK QENVEAEASM VIAVPEPFGG AIIIGQESIT YH NGDKYLA IAPPIIKQST IVCHNRVDPN GSRYLLGDME GRLFMLLLEK EEQMDGTVTL KDLRVELLGE TSIAECLTYL DNG VVFVGS RLGDSQLVKL NVDSNEQGSY VVAMETFTNL GPIVDMCVVD LERQGQGQLV TCSGAFKEGS LRIIRNGIGI HEHA SIDLP GIKGLWPLRS DPNRETDDTL VLSFVGQTRV LMLNGEEVEE TELMGFVDDQ QTFFCGNVAH QQLIQITSAS VRLVS QEPK ALVSEWKEPQ AKNISVASCN SSQVVVAVGR ALYYLQIHPQ ELRQISHTEM EHEVACLDIT PLGDSNGLSP LCAIGL WTD ISARILKLPS FELLHKEMLG GEIIPRSILM TTFESSHYLL CALGDGALFY FGLNIETGLL SDRKKVTLGT QPTVLRT FR SLSTTNVFAC SDRPTVIYSS NHKLVFSNVN LKEVNYMCPL NSDGYPDSLA LANNSTLTIG TIDEIQKLHI RTVPLYES P RKICYQEVSQ CFGVLSSRIE VQDTSGGTTA LRPSASTQAL SSSVSSSKLF SSSTAPHETS FGEEVEVHNL LIIDQHTFE VLHAHQFLQN EYALSLVSCK LGKDPNTYFI VGTAMVYPEE AEPKQGRIVV FQYSDGKLQT VAEKEVKGAV YSMVEFNGKL LASINSTVR LYEWTTEKEL RTECNHYNNI MALYLKTKGD FILVGDLMRS VLLLAYKPME GNFEEIARDF NPNWMSAVEI L DDDNFLGA ENAFNLFVCQ KDSAATTDEE RQHLQEVGLF HLGEFVNVFC HGSLVMQNLG ETSTPTQGSV LFGTVNGMIG LV TSLSESW YNLLLDMQNR LNKVIKSVGK IEHSFWRSFH TERKTEPATG FIDGDLIESF LDISRPKMQE VVANLQYDDG SGM KREATA DDLIKVVEEL TRIH

UniProtKB: DNA damage-binding protein 1

-
Macromolecule #7: Cullin-4A

MacromoleculeName: Cullin-4A / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.814297 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MADEAPRKGS FSALVGRTNG LTKPAALAAA PAKPGGAGGS KKLVIKNFRD RPRLPDNYTQ DTWRKLHEAV RAVQSSTSIR YNLEELYQA VENLCSHKVS PMLYKQLRQA CEDHVQAQIL PFREDSLDSV LFLKKINTCW QDHCRQMIMI RSIFLFLDRT Y VLQNSTLP ...String:
MADEAPRKGS FSALVGRTNG LTKPAALAAA PAKPGGAGGS KKLVIKNFRD RPRLPDNYTQ DTWRKLHEAV RAVQSSTSIR YNLEELYQA VENLCSHKVS PMLYKQLRQA CEDHVQAQIL PFREDSLDSV LFLKKINTCW QDHCRQMIMI RSIFLFLDRT Y VLQNSTLP SIWDMGLELF RTHIISDKMV QSKTIDGILL LIERERSGEA VDRSLLRSLL GMLSDLQVYK DSFELKFLEE TN CLYAAEG QRLMQEREVP EYLNHVSKRL EEEGDRVITY LDHSTQKPLI ACVEKQLLGE HLTAILQKGL DHLLDENRVP DLA QMYQLF SRVRGGQQAL LQHWSEYIKT FGTAIVINPE KDKDMVQDLL DFKDKVDHVI EVCFQKNERF VNLMKESFET FINK RPNKP AELIAKHVDS KLRAGNKEAT DEELERTLDK IMILFRFIHG KDVFEAFYKK DLAKRLLVGK SASVDAEKSM LSKLK HECG AAFTSKLEGM FKDMELSKDI MVHFKQHMQN QSDSGPIDLT VNILTMGYWP TYTPMEVHLT PEMIKLQEVF KAFYLG KHS GRKLQWQTTL GHAVLKAEFK EGKKEFQVSL FQTLVLLMFN EGDGFSFEEI KMATGIEDSE LRRTLQSLAC GKARVLI KS PKGKEVEDGD KFIFNGEFKH KLFRIKINQI QMKETVEEQV STTERVFQDR QYQIDAAIVR IMKMRKTLGH NLLVSELY N QLKFPVKPGD LKKRIESLID RDYMERDKDN PNQYHYVA

UniProtKB: Cullin-4A

-
Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 42.0 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: 0.15 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab Initio in CryoSPARC.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 82975
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: ANGULAR RECONSTITUTION
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