[English] 日本語
Yorodumi
- EMDB-40683: High resolution structure of ESRRB nucleosome bound OCT4 at site ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-40683
TitleHigh resolution structure of ESRRB nucleosome bound OCT4 at site a and site b
Map data
Sample
  • Complex: Complex of ESRRB nucleosome bound to OCT4
    • DNA: DNA (168-MER)
    • DNA: DNA (168-MER)
    • Protein or peptide: Maltodextrin-binding protein,POU domain, class 5, transcription factor 1
    • Protein or peptide: Histone H3.1Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 2-C
    • Protein or peptide: Histone H2B type 2-E
    • Protein or peptide: ScFvSingle-chain variable fragment
Keywordsnucleosome / transcription factor / transcription / CHROMATIN BINDING PROTEIN-DNA complex / GENE REGULATION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


cell fate commitment involved in formation of primary germ layer / cardiac cell fate determination / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / endodermal-mesodermal cell signaling / regulation of asymmetric cell division / endodermal cell fate specification / Specification of primordial germ cells / heart induction / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation ...cell fate commitment involved in formation of primary germ layer / cardiac cell fate determination / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / endodermal-mesodermal cell signaling / regulation of asymmetric cell division / endodermal cell fate specification / Specification of primordial germ cells / heart induction / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Transcriptional regulation of pluripotent stem cells / regulation of DNA methylation-dependent heterochromatin formation / Germ layer formation at gastrulation / miRNA binding / somatic stem cell population maintenance / blastocyst development / carbohydrate transmembrane transporter activity / anatomical structure morphogenesis / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / BMP signaling pathway / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / epigenetic regulation of gene expression / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / negative regulation of miRNA transcription / SIRT1 negatively regulates rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / DNA-binding transcription repressor activity, RNA polymerase II-specific / nucleosome assembly / response to wounding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / positive regulation of canonical Wnt signaling pathway / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / sequence-specific double-stranded DNA binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / outer membrane-bounded periplasmic space / chromatin organization / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / HATs acetylate histones / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / chromosome, telomeric region / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / defense response to Gram-positive bacterium / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding
Similarity search - Function
POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain signature 1. / POU-specific (POUs) domain signature 2. / POU-specific (POUs) domain profile. / Found in Pit-Oct-Unc transcription factors / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain ...POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain signature 1. / POU-specific (POUs) domain signature 2. / POU-specific (POUs) domain profile. / Found in Pit-Oct-Unc transcription factors / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Lambda repressor-like, DNA-binding domain superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Homeobox-like domain superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Maltodextrin-binding protein / Histone H4 / Histone H3.1 / POU domain, class 5, transcription factor 1 / Histone H2A type 2-C / Histone H2B type 2-E
Similarity search - Component
Biological speciesHomo sapiens (human) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLian T / Guan R / Bai Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Mol Cell / Year: 2023
Title: Structural mechanism of LIN28B nucleosome targeting by OCT4.
Authors: Ruifang Guan / Tengfei Lian / Bing-Rui Zhou / David Wheeler / Yawen Bai /
Abstract: Pioneer transcription factors are essential for cell fate changes by targeting closed chromatin. OCT4 is a crucial pioneer factor that can induce cell reprogramming. However, the structural basis of ...Pioneer transcription factors are essential for cell fate changes by targeting closed chromatin. OCT4 is a crucial pioneer factor that can induce cell reprogramming. However, the structural basis of how pioneer factors recognize the in vivo nucleosomal DNA targets is unknown. Here, we determine the high-resolution structures of the nucleosome containing human LIN28B DNA and its complexes with the OCT4 DNA binding region. Three OCT4s bind the pre-positioned nucleosome by recognizing non-canonical DNA sequences. Two use their POUS domains while the other uses the POUS-loop-POUHD region; POUHD serves as a wedge to unwrap ∼25 base pair DNA. Our analysis of previous genomic data and determination of the ESRRB-nucleosome-OCT4 structure confirmed the generality of these structural features. Moreover, biochemical studies suggest that multiple OCT4s cooperatively open the H1-condensed nucleosome array containing the LIN28B nucleosome. Thus, our study suggests a mechanism of how OCT4 can target the nucleosome and open closed chromatin.
History
DepositionMay 3, 2023-
Header (metadata) releaseJun 28, 2023-
Map releaseJun 28, 2023-
UpdateJun 28, 2023-
Current statusJun 28, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_40683.png

Downloads & links

-
Map

FileDownload / File: emd_40683.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.056 Å
Density
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.6449656 - 1.4959065
Average (Standard dev.)0.00313058 (±0.05059063)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 253.44 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_40683_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_40683_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of ESRRB nucleosome bound to OCT4

EntireName: Complex of ESRRB nucleosome bound to OCT4
Components
  • Complex: Complex of ESRRB nucleosome bound to OCT4
    • DNA: DNA (168-MER)
    • DNA: DNA (168-MER)
    • Protein or peptide: Maltodextrin-binding protein,POU domain, class 5, transcription factor 1
    • Protein or peptide: Histone H3.1Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 2-C
    • Protein or peptide: Histone H2B type 2-E
    • Protein or peptide: ScFvSingle-chain variable fragment

-
Supramolecule #1: Complex of ESRRB nucleosome bound to OCT4

SupramoleculeName: Complex of ESRRB nucleosome bound to OCT4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: DNA (168-MER)

MacromoleculeName: DNA (168-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.499562 KDa
SequenceString: (DA)(DT)(DC)(DA)(DG)(DC)(DA)(DG)(DG)(DG) (DA)(DG)(DA)(DA)(DG)(DG)(DA)(DG)(DC)(DG) (DC)(DC)(DT)(DC)(DC)(DC)(DC)(DA)(DT) (DG)(DT)(DG)(DG)(DG)(DA)(DC)(DC)(DT)(DG) (DG) (DA)(DG)(DA)(DA)(DA)(DC) ...String:
(DA)(DT)(DC)(DA)(DG)(DC)(DA)(DG)(DG)(DG) (DA)(DG)(DA)(DA)(DG)(DG)(DA)(DG)(DC)(DG) (DC)(DC)(DT)(DC)(DC)(DC)(DC)(DA)(DT) (DG)(DT)(DG)(DG)(DG)(DA)(DC)(DC)(DT)(DG) (DG) (DA)(DG)(DA)(DA)(DA)(DC)(DA)(DG) (DA)(DG)(DG)(DG)(DT)(DG)(DG)(DA)(DG)(DG) (DG)(DA) (DG)(DC)(DA)(DT)(DA)(DG)(DA) (DG)(DA)(DG)(DT)(DC)(DT)(DG)(DT)(DT)(DC) (DT)(DA)(DA) (DG)(DC)(DT)(DG)(DC)(DA) (DA)(DA)(DG)(DC)(DA)(DA)(DA)(DG)(DG)(DC) (DC)(DT)(DG)(DG) (DC)(DG)(DA)(DC)(DC) (DT)(DA)(DG)(DG)(DA)(DG)(DA)(DC)(DC)(DA) (DT)(DG)(DG)(DA)(DG) (DT)(DT)(DC)(DC) (DA)(DG)(DA)(DA)(DA)(DG)(DT)(DG)(DA)(DT) (DA)(DG)(DT)(DT)(DA)(DT) (DG)(DC)(DA) (DG)(DA)(DG)(DC)(DG)(DA)(DA)(DT)(DG)(DG) (DA)(DG)(DG)(DG)(DA)(DA)(DT) (DC)(DA) (DG)(DC)(DA)(DC)(DG)(DC)

-
Macromolecule #2: DNA (168-MER)

MacromoleculeName: DNA (168-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.224516 KDa
SequenceString: (DG)(DC)(DG)(DT)(DG)(DC)(DT)(DG)(DA)(DT) (DT)(DC)(DC)(DC)(DT)(DC)(DC)(DA)(DT)(DT) (DC)(DG)(DC)(DT)(DC)(DT)(DG)(DC)(DA) (DT)(DA)(DA)(DC)(DT)(DA)(DT)(DC)(DA)(DC) (DT) (DT)(DT)(DC)(DT)(DG)(DG) ...String:
(DG)(DC)(DG)(DT)(DG)(DC)(DT)(DG)(DA)(DT) (DT)(DC)(DC)(DC)(DT)(DC)(DC)(DA)(DT)(DT) (DC)(DG)(DC)(DT)(DC)(DT)(DG)(DC)(DA) (DT)(DA)(DA)(DC)(DT)(DA)(DT)(DC)(DA)(DC) (DT) (DT)(DT)(DC)(DT)(DG)(DG)(DA)(DA) (DC)(DT)(DC)(DC)(DA)(DT)(DG)(DG)(DT)(DC) (DT)(DC) (DC)(DT)(DA)(DG)(DG)(DT)(DC) (DG)(DC)(DC)(DA)(DG)(DG)(DC)(DC)(DT)(DT) (DT)(DG)(DC) (DT)(DT)(DT)(DG)(DC)(DA) (DG)(DC)(DT)(DT)(DA)(DG)(DA)(DA)(DC)(DA) (DG)(DA)(DC)(DT) (DC)(DT)(DC)(DT)(DA) (DT)(DG)(DC)(DT)(DC)(DC)(DC)(DT)(DC)(DC) (DA)(DC)(DC)(DC)(DT) (DC)(DT)(DG)(DT) (DT)(DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG)(DT) (DC)(DC)(DC)(DA)(DC)(DA) (DT)(DG)(DG) (DG)(DG)(DA)(DG)(DG)(DC)(DG)(DC)(DT)(DC) (DC)(DT)(DT)(DC)(DT)(DC)(DC) (DC)(DT) (DG)(DC)(DT)(DG)(DA)(DT)

-
Macromolecule #3: Maltodextrin-binding protein,POU domain, class 5, transcription f...

MacromoleculeName: Maltodextrin-binding protein,POU domain, class 5, transcription factor 1
type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.285703 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MKEAKIEEGK LVIWINGDKG YNGLAEVGKK FEKDTGIKVT VEHPDKLEEK FPQVAATGDG PDIIFWAHDR FGGYAQSGLL AEITPDKAF QDKLYPFTWD AVRYNGKLIA YPIAVEALSL IYNKDLLPNP PKTWEEIPAL DKELKAKGKS ALMFNLQEPY F TWPLIAAD ...String:
MKEAKIEEGK LVIWINGDKG YNGLAEVGKK FEKDTGIKVT VEHPDKLEEK FPQVAATGDG PDIIFWAHDR FGGYAQSGLL AEITPDKAF QDKLYPFTWD AVRYNGKLIA YPIAVEALSL IYNKDLLPNP PKTWEEIPAL DKELKAKGKS ALMFNLQEPY F TWPLIAAD GGYAFKYENG KYDIKDVGVD NAGAKAGLTF LVDLIKNKHM NADTDYSIAE AAFNKGETAM TINGPWAWSN ID TSKVNYG VTVLPTFKGQ PSKPFVGVLS AGINAASPNK ELAKEFLENY LLTDEGLEAV NKDKPLGAVA LKSYEEELAK DPR IAATME NAQKGEIMPN IPQMSAFWYA VRTAVINAAS GRQTVDAALA AAQTNAGSEN LYFQGSVDSA AASDIKALQK ELEQ FAKLL KQKRITLGYT QADVGLTLGV LFGKVFSQTT ICRFEALQLS FKNMCKLRPL LQKWVEEADN NENLQEICKA ETLVQ ARKR KRTSIENRVR GNLENLFLQC PKPTLQQISH IAQQLGLEKD VVRVWFCNRR QKGKRSSSEF HHHHHH

-
Macromolecule #4: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.437167 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

-
Macromolecule #5: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

-
Macromolecule #6: Histone H2A type 2-C

MacromoleculeName: Histone H2A type 2-C / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.017428 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MSGRGKQGGK ARAKAKSRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YMAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG KVTIAQGGVL PNIQAVLLPK KTESHKAKSK

-
Macromolecule #7: Histone H2B type 2-E

MacromoleculeName: Histone H2B type 2-E / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.951239 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSSK

-
Macromolecule #8: ScFv

MacromoleculeName: ScFv / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 29.030146 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MKSSHHHHHH ENLYFQSNAM EVQLQQSGPE LVEPGTSVKM PCKASGYTFT SYTIQWVKQT PRQGLEWIGY IYPYNAGTKY NEKFKGKAT LTSDKSSSTV YMELSSLTSE DSAVYYCARK SSRLRSTLDY WGQGTSVTVS SGGGGSGGGG SGGGGSMDIK M TQSPSSMH ...String:
MKSSHHHHHH ENLYFQSNAM EVQLQQSGPE LVEPGTSVKM PCKASGYTFT SYTIQWVKQT PRQGLEWIGY IYPYNAGTKY NEKFKGKAT LTSDKSSSTV YMELSSLTSE DSAVYYCARK SSRLRSTLDY WGQGTSVTVS SGGGGSGGGG SGGGGSMDIK M TQSPSSMH ASLGERVTIT CKASQDIRSY LSWYQQKPWK SPKTLIYYAT SLADGVPSRF SGSGSGQDFS LTINNLESDD TA TYYCLQH GESPYTFGSG TKLEIKRA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.3
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 68790

+
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