[English] 日本語
Yorodumi
- PDB-7vbm: The mouse nucleosome structure containing H3mm18 aided by PL2-6 scFv -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vbm
TitleThe mouse nucleosome structure containing H3mm18 aided by PL2-6 scFv
Components
  • (DNA (126-MER)) x 2
  • Histone H2A type 1-B
  • Histone H2B type 3-A
  • Histone H3mm18
  • Histone H4
KeywordsDNA BINDING PROTEIN / complex / chromatin / nucleosome / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Inhibition of DNA recombination at telomere / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected purine / Condensation of Prophase Chromosomes / Cleavage of the damaged purine / SUMOylation of chromatin organization proteins / DNA Damage/Telomere Stress Induced Senescence / NoRC negatively regulates rRNA expression / SIRT1 negatively regulates rRNA expression / G2/M DNA damage checkpoint ...Inhibition of DNA recombination at telomere / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected purine / Condensation of Prophase Chromosomes / Cleavage of the damaged purine / SUMOylation of chromatin organization proteins / DNA Damage/Telomere Stress Induced Senescence / NoRC negatively regulates rRNA expression / SIRT1 negatively regulates rRNA expression / G2/M DNA damage checkpoint / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / RNA Polymerase I Promoter Escape / Processing of DNA double-strand break ends / HDMs demethylate histones / Transcriptional regulation by small RNAs / Metalloprotease DUBs / B-WICH complex positively regulates rRNA expression / Nonhomologous End-Joining (NHEJ) / HDACs deacetylate histones / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / UCH proteinases / Senescence-Associated Secretory Phenotype (SASP) / PRC2 methylates histones and DNA / HATs acetylate histones / PKMTs methylate histone lysines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / Estrogen-dependent gene expression / Oxidative Stress Induced Senescence / Ub-specific processing proteases / negative regulation of megakaryocyte differentiation / DNA replication-independent chromatin assembly / DNA replication-dependent chromatin assembly / heterochromatin assembly / nuclear chromosome / nucleosome assembly / nucleosome / DNA-templated transcription, initiation / protein heterodimerization activity / protein domain specific binding / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A signature. / Histone H2A conserved site / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H4 signature. ...Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A signature. / Histone H2A conserved site / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H4 signature. / Histone H4, conserved site / 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 / Core histone H2A/H2B/H3/H4 / Histone H2A/H2B/H3 / Histone-fold
Similarity search - Domain/homology
DNA (> 100) / DNA / DNA (> 10) / Histone H2A type 1-B / Histone H4 / H2B.U histone 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsHirai, S. / Takizawa, Y. / Kujirai, T. / Kurumizaka, H.
Funding support Japan, 12items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR16G1 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05534 Japan
Japan Society for the Promotion of Science (JSPS)JP18K14677 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05527 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05244 Japan
Japan Society for the Promotion of Science (JSPS)JP19K06522 Japan
Japan Society for the Promotion of Science (JSPS)JP20H00456 Japan
Japan Society for the Promotion of Science (JSPS)JP20H04846 Japan
Japan Society for the Promotion of Science (JSPS)JP20H00449 Japan
Japan Science and TechnologyJPMJER1901 Japan
Japan Society for the Promotion of Science (JSPS)JP20K15711 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101076 Japan
CitationJournal: Nucleic Acids Res / Year: 2022
Title: Unusual nucleosome formation and transcriptome influence by the histone H3mm18 variant.
Authors: Seiya Hirai / Kosuke Tomimatsu / Atsuko Miyawaki-Kuwakado / Yoshimasa Takizawa / Tetsuro Komatsu / Taro Tachibana / Yutaro Fukushima / Yasuko Takeda / Lumi Negishi / Tomoya Kujirai / Masako ...Authors: Seiya Hirai / Kosuke Tomimatsu / Atsuko Miyawaki-Kuwakado / Yoshimasa Takizawa / Tetsuro Komatsu / Taro Tachibana / Yutaro Fukushima / Yasuko Takeda / Lumi Negishi / Tomoya Kujirai / Masako Koyama / Yasuyuki Ohkawa / Hitoshi Kurumizaka /
Abstract: Histone H3mm18 is a non-allelic H3 variant expressed in skeletal muscle and brain in mice. However, its function has remained enigmatic. We found that H3mm18 is incorporated into chromatin in cells ...Histone H3mm18 is a non-allelic H3 variant expressed in skeletal muscle and brain in mice. However, its function has remained enigmatic. We found that H3mm18 is incorporated into chromatin in cells with low efficiency, as compared to H3.3. We determined the structures of the nucleosome core particle (NCP) containing H3mm18 by cryo-electron microscopy, which revealed that the entry/exit DNA regions are drastically disordered in the H3mm18 NCP. Consistently, the H3mm18 NCP is substantially unstable in vitro. The forced expression of H3mm18 in mouse myoblast C2C12 cells markedly suppressed muscle differentiation. A transcriptome analysis revealed that the forced expression of H3mm18 affected the expression of multiple genes, and suppressed a group of genes involved in muscle development. These results suggest a novel gene expression regulation system in which the chromatin landscape is altered by the formation of unusual nucleosomes with a histone variant, H3mm18, and provide important insight into understanding transcription regulation by chromatin.
History
DepositionAug 31, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-31882
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone H3mm18
B: Histone H4
C: Histone H2A type 1-B
D: Histone H2B type 3-A
E: Histone H3mm18
F: Histone H4
G: Histone H2A type 1-B
H: Histone H2B type 3-A
I: DNA (126-MER)
J: DNA (126-MER)


Theoretical massNumber of molelcules
Total (without water)201,07810
Polymers201,07810
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H3mm18


Mass: 15350.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Protein Histone H4 /


Mass: 11676.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Gene: Hist1h4a, Hist1h4b, H4-53, Hist1h4c, H4-12, Hist1h4d, Hist1h4f, Hist1h4h, Hist1h4i, Hist1h4j, Hist1h4k, Hist1h4m, Hist2h4a, Hist2h4, Hist4h4
Production host: Escherichia coli (E. coli) / References: UniProt: P62806
#3: Protein Histone H2A type 1-B


Mass: 14447.825 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hist1h2ab / Production host: Escherichia coli (E. coli) / References: UniProt: C0HKE1
#4: Protein Histone H2B type 3-A


Mass: 14307.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hist3h2ba / Production host: Escherichia coli (E. coli) / References: UniProt: Q9D2U9

-
DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (126-MER)


Mass: 44520.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#6: DNA chain DNA (126-MER)


Mass: 44991.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: The mouse nucleosome containing H3mm18 aided by PL2-6 scFv
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 58.1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 224465 / Symmetry type: POINT

+
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