[English] 日本語
Yorodumi
- EMDB-33533: Cryo-EM structure of the nucleosome in complex with p53 DNA-bindi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-33533
TitleCryo-EM structure of the nucleosome in complex with p53 DNA-binding domain
Map dataCryo-EM structure of the nucleosome in complex with p53 DNA-binding domains
Sample
  • Complex: Cryo-EM structure of the nucleosome in complex with p53 DNA-binding domain
    • Complex: nucleosome with p53
      • Protein or peptide: Histone H3.1
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1-B/E
      • Protein or peptide: Histone H2B type 1-J
      • Protein or peptide: Cellular tumor antigen p53
    • Complex: DNA (193-MER)
      • DNA: DNA (193-MER)
      • DNA: DNA (193-MER)
KeywordsTranscription factor / Tumor-suppressor / GENE REGULATION / GENE REGURATION-DNA complex
Function / homology
Function and homology information


Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity ...Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / regulation of tissue remodeling / glucose catabolic process to lactate via pyruvate / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / germ cell nucleus / T cell lineage commitment / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / regulation of DNA damage response, signal transduction by p53 class mediator / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / B cell lineage commitment / thymocyte apoptotic process / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / mitochondrial DNA repair / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / TP53 Regulates Transcription of Caspase Activators and Caspases / ER overload response / positive regulation of release of cytochrome c from mitochondria / negative regulation of DNA replication / positive regulation of cardiac muscle cell apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / entrainment of circadian clock by photoperiod / cardiac septum morphogenesis / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / necroptotic process / Zygotic genome activation (ZGA) / positive regulation of execution phase of apoptosis / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / rRNA transcription / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / response to X-ray / replicative senescence / Pyroptosis / negative regulation of tumor necrosis factor-mediated signaling pathway / mitophagy / cellular response to UV-C / positive regulation of RNA polymerase II transcription preinitiation complex assembly / neuroblast proliferation / hematopoietic stem cell differentiation / negative regulation of reactive oxygen species metabolic process / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / somitogenesis / embryonic organ development / chromosome organization / T cell proliferation involved in immune response / negative regulation of megakaryocyte differentiation / type II interferon-mediated signaling pathway / glial cell proliferation / viral process / cis-regulatory region sequence-specific DNA binding / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / protein localization to CENP-A containing chromatin / hematopoietic progenitor cell differentiation / cellular response to actinomycin D / Chromatin modifying enzymes / positive regulation of intrinsic apoptotic signaling pathway / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / cellular response to glucose starvation / core promoter sequence-specific DNA binding / negative regulation of stem cell proliferation / mitotic G1 DNA damage checkpoint signaling / Packaging Of Telomere Ends / negative regulation of fibroblast proliferation
Similarity search - Function
Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family ...Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / 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 H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / Histone H2A / Histone 2A / 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 / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Cellular tumor antigen p53 / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.53 Å
AuthorsNishimura M / Nozawa K / Takizawa Y / Kurumizaka H
Funding support Japan, 10 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19J23094 Japan
Japan Society for the Promotion of Science (JSPS)JP19K06522 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05534 Japan
Japan Society for the Promotion of Science (JSPS)JP20H00449 Japan
Japan Society for the Promotion of Science (JSPS)JP20K06599 Japan
Japan Society for the Promotion of Science (JSPS)JP21H05154 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101076 Japan
Japan Agency for Medical Research and Development (AMED)JP22ama121009 Japan
Japan Science and TechnologyJPMJPR18K9 Japan
Japan Science and TechnologyJPMJER1901 Japan
CitationJournal: PNAS Nexus / Year: 2022
Title: Structural basis for p53 binding to its nucleosomal target DNA sequence.
Authors: Masahiro Nishimura / Yoshimasa Takizawa / Kayo Nozawa / Hitoshi Kurumizaka /
Abstract: The tumor suppressor p53 functions as a pioneer transcription factor that binds a nucleosomal target DNA sequence. However, the mechanism by which p53 binds to its target DNA in the nucleosome ...The tumor suppressor p53 functions as a pioneer transcription factor that binds a nucleosomal target DNA sequence. However, the mechanism by which p53 binds to its target DNA in the nucleosome remains elusive. Here we report the cryo-electron microscopy structures of the p53 DNA-binding domain and the full-length p53 protein complexed with a nucleosome containing the 20 base-pair target DNA sequence of p53 (p53BS). In the p53-nucleosome structures, the p53 DNA-binding domain forms a tetramer and specifically binds to the p53BS DNA, located near the entry/exit region of the nucleosome. The nucleosomal position of the p53BS DNA is within the genomic p21 promoter region. The p53 binding peels the DNA from the histone surface, and drastically changes the DNA path around the p53BS on the nucleosome. The C-terminal domain of p53 also binds to the DNA around the center and linker DNA regions of the nucleosome, as revealed by hydroxyl radical footprinting. These results provide important structural information for understanding the mechanism by which p53 binds the nucleosome and changes the chromatin structure for gene activation.
History
DepositionJun 3, 2022-
Header (metadata) releaseOct 12, 2022-
Map releaseOct 12, 2022-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_33533.png

Downloads & links

-
Map

FileDownload / File: emd_33533.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the nucleosome in complex with p53 DNA-binding domains
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 220 pix.
= 242. Å		1.1 Å/pix.
x 220 pix.
= 242. Å		1.1 Å/pix.
x 220 pix.
= 242. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.012964697 - 0.043672733
Average (Standard dev.)0.00056367525 (±0.00270603)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 242.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_33533_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_33533_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Cryo-EM structure of the nucleosome in complex with p53 DNA-bindi...

EntireName: Cryo-EM structure of the nucleosome in complex with p53 DNA-binding domain
Components
  • Complex: Cryo-EM structure of the nucleosome in complex with p53 DNA-binding domain
    • Complex: nucleosome with p53
      • Protein or peptide: Histone H3.1
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1-B/E
      • Protein or peptide: Histone H2B type 1-J
      • Protein or peptide: Cellular tumor antigen p53
    • Complex: DNA (193-MER)
      • DNA: DNA (193-MER)
      • DNA: DNA (193-MER)

+
Supramolecule #1: Cryo-EM structure of the nucleosome in complex with p53 DNA-bindi...

SupramoleculeName: Cryo-EM structure of the nucleosome in complex with p53 DNA-binding domain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 329 KDa

+
Supramolecule #2: nucleosome with p53

SupramoleculeName: nucleosome with p53 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4, #7

+
Supramolecule #3: DNA (193-MER)

SupramoleculeName: DNA (193-MER) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6

+
Macromolecule #1: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.719445 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMARTKQT ARKSTGGKAP RKQLATKAAR KSAPATGGVK KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQ SSAVMALQEA CEAYLVGLFE DTNLCAIHAK RVTIMPKDIQ LARRIRGERA

UniProtKB: Histone H3.1

+
Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.676703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGRGKG GKGLGKGGAK RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKVFLENVI RDAVTYTEHA KRKTVTAMD VVYALKRQGR TLYGFGG

UniProtKB: Histone H4

+
Macromolecule #3: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.447825 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSGRGKQ GGKARAKAKT RSSRAGLQFP VGRVHRLLRK GNYSERVGAG APVYLAAVLE YLTAEILELA GNAARDNKKT RIIPRHLQL AIRNDEELNK LLGRVTIAQG GVLPNIQAVL LPKKTESHHK AKGK

UniProtKB: Histone H2A type 1-B/E

+
Macromolecule #4: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.217516 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMPEPAKS APAPKKGSKK AVTKAQKKDG KKRKRSRKES YSIYVYKVLK QVHPDTGISS KAMGIMNSFV NDIFERIAGE ASRLAHYNK RSTITSREIQ TAVRLLLPGE LAKHAVSEGT KAVTKYTSAK

UniProtKB: Histone H2B type 1-J

+
Macromolecule #7: Cellular tumor antigen p53

MacromoleculeName: Cellular tumor antigen p53 / type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.65975 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPSSSVPSQK TYQGSYGFRL GFLHSGTAKS VTCTYSPALN KMFCQLAKTC PVQLWVDSTP PPGTRVRAMA IYKQSQHMTE VVRRCPHHE RCSDSDGLAP PQHLIRVEGN LRVEYLDDRN TFRHSVVVPY EPPEVGSDCT TIHYNYMCNS SCMGGMNRRP I LTIITLED ...String:
GPSSSVPSQK TYQGSYGFRL GFLHSGTAKS VTCTYSPALN KMFCQLAKTC PVQLWVDSTP PPGTRVRAMA IYKQSQHMTE VVRRCPHHE RCSDSDGLAP PQHLIRVEGN LRVEYLDDRN TFRHSVVVPY EPPEVGSDCT TIHYNYMCNS SCMGGMNRRP I LTIITLED SSGNLLGRNS FEVRVCACPG RDRRTEEENL RKKG

UniProtKB: Cellular tumor antigen p53

+
Macromolecule #5: DNA (193-MER)

MacromoleculeName: DNA (193-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 59.417824 KDa
SequenceString: (DA)(DT)(DC)(DG)(DG)(DA)(DC)(DC)(DC)(DT) (DA)(DT)(DC)(DG)(DC)(DG)(DA)(DG)(DC)(DC) (DA)(DG)(DG)(DC)(DC)(DT)(DG)(DA)(DG) (DA)(DA)(DT)(DC)(DC)(DG)(DG)(DT)(DG)(DC) (DC) (DG)(DA)(DG)(DG)(DC)(DC) ...String:
(DA)(DT)(DC)(DG)(DG)(DA)(DC)(DC)(DC)(DT) (DA)(DT)(DC)(DG)(DC)(DG)(DA)(DG)(DC)(DC) (DA)(DG)(DG)(DC)(DC)(DT)(DG)(DA)(DG) (DA)(DA)(DT)(DC)(DC)(DG)(DG)(DT)(DG)(DC) (DC) (DG)(DA)(DG)(DG)(DC)(DC)(DG)(DC) (DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC) (DG)(DT) (DA)(DG)(DA)(DC)(DA)(DG)(DC) (DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC)(DG) (DC)(DT)(DT) (DA)(DA)(DA)(DC)(DG)(DC) (DA)(DC)(DG)(DT)(DA)(DC)(DG)(DC)(DG)(DC) (DT)(DG)(DT)(DC) (DC)(DC)(DC)(DC)(DG) (DC)(DG)(DT)(DT)(DT)(DT)(DA)(DA)(DC)(DC) (DG)(DC)(DC)(DA)(DA) (DG)(DG)(DG)(DG) (DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC)(DC)(DT) (DA)(DG)(DT)(DC)(DT)(DC) (DC)(DA)(DG) (DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC)(DA) (DG)(DA)(DT)(DA)(DT)(DA)(DG) (DG)(DG) (DC)(DA)(DT)(DG)(DT)(DC)(DC)(DG)(DG)(DG) (DC)(DA)(DT)(DG)(DT)(DC)(DC)(DC) (DG) (DA)(DA)(DA)(DT)(DT)(DC)(DA)(DT)(DA)(DG) (DA)(DT)

+
Macromolecule #6: DNA (193-MER)

MacromoleculeName: DNA (193-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 59.760027 KDa
SequenceString: (DA)(DT)(DC)(DT)(DA)(DT)(DG)(DA)(DA)(DT) (DT)(DT)(DC)(DG)(DG)(DG)(DA)(DC)(DA)(DT) (DG)(DC)(DC)(DC)(DG)(DG)(DA)(DC)(DA) (DT)(DG)(DC)(DC)(DC)(DT)(DA)(DT)(DA)(DT) (DC) (DT)(DG)(DA)(DC)(DA)(DC) ...String:
(DA)(DT)(DC)(DT)(DA)(DT)(DG)(DA)(DA)(DT) (DT)(DT)(DC)(DG)(DG)(DG)(DA)(DC)(DA)(DT) (DG)(DC)(DC)(DC)(DG)(DG)(DA)(DC)(DA) (DT)(DG)(DC)(DC)(DC)(DT)(DA)(DT)(DA)(DT) (DC) (DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT) (DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC) (DT)(DA) (DG)(DG)(DG)(DA)(DG)(DT)(DA) (DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG) (DC)(DG)(DG) (DT)(DT)(DA)(DA)(DA)(DA) (DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC) (DA)(DG)(DC)(DG) (DC)(DG)(DT)(DA)(DC) (DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA) (DG)(DC)(DG)(DG)(DT) (DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA) (DC)(DG)(DA)(DC)(DC)(DA) (DA)(DT)(DT) (DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC) (DG)(DG)(DC)(DA)(DC)(DC)(DG) (DG)(DA) (DT)(DT)(DC)(DT)(DC)(DA)(DG)(DG)(DC)(DC) (DT)(DG)(DG)(DC)(DT)(DC)(DG)(DC) (DG) (DA)(DT)(DA)(DG)(DG)(DG)(DT)(DC)(DC)(DG) (DA)(DT)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
10.0 mMC8H19KN2O5SHEPES-KOH
2.0 mMC9H15O6PTCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2452876
Startup modelType of model: EMDB MAP
EMDB ID:

3657

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.53 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.2) / Number images used: 53958
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.2)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

7ohc

source_name: PDB, initial_model_type: experimental model

3kmd

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL
Output model

PDB-7xzx:
Cryo-EM structure of the nucleosome in complex with p53 DNA-binding domain

+
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