[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

TitleBasis of the H2AK119 specificity of the Polycomb repressive deubiquitinase.
Journal, issue, pagesNature, Vol. 616, Issue 7955, Page 176-182, Year 2023
Publish dateMar 29, 2023
AuthorsWeiran Ge / Cong Yu / Jingjing Li / Zhenyu Yu / Xiaorong Li / Yan Zhang / Chao-Pei Liu / Yingfeng Li / Changlin Tian / Xinzheng Zhang / Guohong Li / Bing Zhu / Rui-Ming Xu /
PubMed AbstractRepression of gene expression by protein complexes of the Polycomb group is a fundamental mechanism that governs embryonic development and cell-type specification. The Polycomb repressive ...Repression of gene expression by protein complexes of the Polycomb group is a fundamental mechanism that governs embryonic development and cell-type specification. The Polycomb repressive deubiquitinase (PR-DUB) complex removes the ubiquitin moiety from monoubiquitinated histone H2A K119 (H2AK119ub1) on the nucleosome, counteracting the ubiquitin E3 ligase activity of Polycomb repressive complex 1 (PRC1) to facilitate the correct silencing of genes by Polycomb proteins and safeguard active genes from inadvertent silencing by PRC1 (refs. ). The intricate biological function of PR-DUB requires accurate targeting of H2AK119ub1, but PR-DUB can deubiquitinate monoubiquitinated free histones and peptide substrates indiscriminately; the basis for its exquisite nucleosome-dependent substrate specificity therefore remains unclear. Here we report the cryo-electron microscopy structure of human PR-DUB, composed of BAP1 and ASXL1, in complex with the chromatosome. We find that ASXL1 directs the binding of the positively charged C-terminal extension of BAP1 to nucleosomal DNA and histones H3-H4 near the dyad, an addition to its role in forming the ubiquitin-binding cleft. Furthermore, a conserved loop segment of the catalytic domain of BAP1 is situated near the H2A-H2B acidic patch. This distinct nucleosome-binding mode displaces the C-terminal tail of H2A from the nucleosome surface, and endows PR-DUB with the specificity for H2AK119ub1.
External linksNature / PubMed:36991118
MethodsEM (single particle)
Resolution2.75 - 4.5 Å
Structure data

34431

8h1t

EMDB-34431, PDB-8h1t:
Cryo-EM structure of BAP1-ASXL1 bound to chromatosome
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-34432: Cryo-EM structure of BAP1-ASXL1 bound to nucleosome
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-35179: Constituent map of cryo-EM structure of BAP1-ASXL1 bound to chromatosome
Method: EM (single particle) / Resolution: 2.75 Å

EMDB-35180: Constituent map of cryo-EM structure of BAP1-ASXL1 bound to chromatosome
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-35181: Constituent map of cryo-EM structure of BAP1-ASXL1 bound to chromatosome
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-35182: Consensus map of cryo-EM structure of BAP1-ASXL1 bound to chromatosome
Method: EM (single particle) / Resolution: 4.5 Å

Source
  • homo sapiens (human)
KeywordsGENE REGULATION / nucleosome / histone deubiquitination / chromatin

+
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