[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleContributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II.
Journal, issue, pagesNucleic Acids Res, Vol. 51, Issue 19, Page 10364-10374, Year 2023
Publish dateOct 27, 2023
AuthorsTakumi Oishi / Suguru Hatazawa / Tomoya Kujirai / Junko Kato / Yuki Kobayashi / Mitsuo Ogasawara / Munetaka Akatsu / Haruhiko Ehara / Shun-Ichi Sekine / Gosuke Hayashi / Yoshimasa Takizawa / Hitoshi Kurumizaka /
PubMed AbstractThe N-terminal tails of histones protrude from the nucleosome core and are target sites for histone modifications, such as acetylation and methylation. Histone acetylation is considered to enhance ...The N-terminal tails of histones protrude from the nucleosome core and are target sites for histone modifications, such as acetylation and methylation. Histone acetylation is considered to enhance transcription in chromatin. However, the contribution of the histone N-terminal tail to the nucleosome transcription by RNA polymerase II (RNAPII) has not been clarified. In the present study, we reconstituted nucleosomes lacking the N-terminal tail of each histone, H2A, H2B, H3 or H4, and performed RNAPII transcription assays. We found that the N-terminal tail of H3, but not H2A, H2B and H4, functions in RNAPII pausing at the SHL(-5) position of the nucleosome. Consistently, the RNAPII transcription assay also revealed that the nucleosome containing N-terminally acetylated H3 drastically alleviates RNAPII pausing at the SHL(-5) position. In addition, the H3 acetylated nucleosome produced increased amounts of the run-off transcript. These results provide important evidence that the H3 N-terminal tail plays a role in RNAPII pausing at the SHL(-5) position of the nucleosome, and its acetylation directly alleviates this nucleosome barrier.
External linksNucleic Acids Res / PubMed:37718728 / PubMed Central
MethodsEM (single particle)
Resolution2.36 - 3.44 Å
Structure data

36389

8jl9

EMDB-36389, PDB-8jl9:
Cryo-EM structure of the human nucleosome with scFv
Method: EM (single particle) / Resolution: 2.65 Å

36390

8jla

EMDB-36390, PDB-8jla:
Cryo-EM structure of the human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4
Method: EM (single particle) / Resolution: 3.44 Å

36391

8jlb

EMDB-36391, PDB-8jlb:
Cryo-EM structure of the 145 bp human nucleosome containing H3.2 C110A mutant
Method: EM (single particle) / Resolution: 2.36 Å

36393

8jld

EMDB-36393, PDB-8jld:
Cryo-EM structure of the 145 bp human nucleosome containing acetylated H3 tail
Method: EM (single particle) / Resolution: 2.48 Å

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsGENE REGULATION/DNA / nuclear protein / chromatin / GENE REGULATION-DNA COMPLEX

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more