[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

TitleStructural basis for the inhibition of PRC2 by active transcription histone posttranslational modifications.
Journal, issue, pagesNat Struct Mol Biol, Vol. 32, Issue 2, Page 393-404, Year 2025
Publish dateJan 7, 2025
AuthorsTrinity Cookis / Alexandria Lydecker / Paul Sauer / Vignesh Kasinath / Eva Nogales /
PubMed AbstractPolycomb repressive complex 2 (PRC2) trimethylates histone H3 on K27 (H3K27me3) leading to gene silencing that is essential for embryonic development and maintenance of cell identity. PRC2 is ...Polycomb repressive complex 2 (PRC2) trimethylates histone H3 on K27 (H3K27me3) leading to gene silencing that is essential for embryonic development and maintenance of cell identity. PRC2 is regulated by protein cofactors and their crosstalk with histone modifications. Trimethylated histone H3 on K4 (H3K4me3) and K36 (H3K36me3) localize to sites of active transcription and inhibit PRC2 activity through unknown mechanisms. Using cryo-electron microscopy, we reveal that histone H3 tails containing H3K36me3 engage poorly with PRC2 and preclude its effective interaction with chromatin, while H3K4me3 binds to the allosteric site in the EED subunit, acting as an antagonist that competes with activators required for spreading of the H3K27me3 repressive mark. Thus, the location of the H3K4me3 and H3K36me3 modifications along the H3 tail allows them to target two requirements for efficient trimethylation of H3K27 by PRC2. We further show that the JARID2 cofactor modulates PRC2 activity in the presence of these histone modifications.
External linksNat Struct Mol Biol / PubMed:39774834 / PubMed Central
MethodsEM (single particle)
Resolution3.1 - 6.7 Å
Structure data

EMDB-43357, PDB-8vmi:
PRC2_AJ119-450 bound to H3K4me3
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-43358, PDB-8vmj:
H3K4me3 nucleosome bound to PRC2_AJ119-450
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-43359, PDB-8vml:
PRC2_AJ1-450 bound to H3K4me3
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-43360, PDB-8vmn:
H3K4me3 nucleosome bound to PRC2_AJ1-450
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-43361, PDB-8vnv:
PRC2_AJ1-450 bound to H3K36me3 with histone H3 tail engaged
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-43362, PDB-8vnz:
PRC2_AJ1-450 bound to H3K36me3-modified nucleosome with histone H3 tail disengaged
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-43363, PDB-8vo0:
H3K36me3-modified nucleosome bound to PRC2_AJ1-450 with histone H3 tail disengaged
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-43373, PDB-8vob:
H3K36me3-modified nucleosome bound to PRC2_AJ1-450
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-47133: PRC2_AJ119-450, JARID2_107-121 / Nuc_unmodified
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-47135: PRC2 AJ119-450 bound to JARID2 113-121,R115A peptide and unmodified nucleosome
Method: EM (single particle) / Resolution: 6.7 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

Source
  • homo sapiens (human)
  • xenopus laevis (African clawed frog)
KeywordsGENE REGULATION / complex / methyltransferase / histone / epigenetics / GENE REGULATION/DNA / nucleosome / chromatin / GENE REGULATION-DNA complex / histones

+
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