[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

TitleUbiquitinated histone H2B as gatekeeper of the nucleosome acidic patch.
Journal, issue, pagesNucleic Acids Res, Vol. 52, Issue 16, Page 9978-9995, Year 2024
Publish dateSep 9, 2024
AuthorsChad W Hicks / Sanim Rahman / Susan L Gloor / James K Fields / Natalia Ledo Husby / Anup Vaidya / Keith E Maier / Michael Morgan / Michael-Christopher Keogh / Cynthia Wolberger /
PubMed AbstractMonoubiquitination of histones H2B-K120 (H2BK120ub) and H2A-K119 (H2AK119ub) play opposing roles in regulating transcription and chromatin compaction. H2BK120ub is a hallmark of actively transcribed ...Monoubiquitination of histones H2B-K120 (H2BK120ub) and H2A-K119 (H2AK119ub) play opposing roles in regulating transcription and chromatin compaction. H2BK120ub is a hallmark of actively transcribed euchromatin, while H2AK119ub is highly enriched in transcriptionally repressed heterochromatin. Whereas H2BK120ub is known to stimulate the binding or activity of various chromatin-modifying enzymes, this post-translational modification (PTM) also interferes with the binding of several proteins to the nucleosome H2A/H2B acidic patch via an unknown mechanism. Here, we report cryoEM structures of an H2BK120ub nucleosome showing that ubiquitin adopts discrete positions that occlude the acidic patch. Molecular dynamics simulations show that ubiquitin remains stably positioned over this nucleosome region. By contrast, our cryoEM structures of H2AK119ub nucleosomes show ubiquitin adopting discrete positions that minimally occlude the acidic patch. Consistent with these observations, H2BK120ub, but not H2AK119ub, abrogates nucleosome interactions with acidic patch-binding proteins RCC1 and LANA, and single-domain antibodies specific to this region. Our results suggest a mechanism by which H2BK120ub serves as a gatekeeper to the acidic patch and point to distinct roles for histone H2AK119 and H2BK120 ubiquitination in regulating protein binding to nucleosomes.
External linksNucleic Acids Res / PubMed:39149911 / PubMed Central
MethodsEM (single particle)
Resolution2.93 - 3.47 Å
Structure data

29767

8g6g

EMDB-29767, PDB-8g6g:
H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 5
Method: EM (single particle) / Resolution: 2.93 Å

29769

8g6h

EMDB-29769, PDB-8g6h:
H2BK120ub+H3K79me2-modified nucleosome ubiquitin position 6
Method: EM (single particle) / Resolution: 3.06 Å

29778

8g6q

EMDB-29778, PDB-8g6q:
H2AK119ub-modified nucleosome ubiquitin position 1
Method: EM (single particle) / Resolution: 3.41 Å

29781

8g6s

EMDB-29781, PDB-8g6s:
H2AK119ub-modified nucleosome ubiquitin position 2
Method: EM (single particle) / Resolution: 3.47 Å

42898

8v25

EMDB-42898, PDB-8v25:
H2BK120ub-modified nucleosome ubiquitin position 1
Method: EM (single particle) / Resolution: 3.32 Å

42899

8v26

EMDB-42899, PDB-8v26:
H2BK120ub-modified nucleosome ubiquitin position 2
Method: EM (single particle) / Resolution: 3.33 Å

42900

8v27

EMDB-42900, PDB-8v27:
H2BK120ub-modified nucleosome ubiquitin position 3
Method: EM (single particle) / Resolution: 3.34 Å

42901

8v28

EMDB-42901, PDB-8v28:
H2BK120ub-modified nucleosome ubiquitin position 4
Method: EM (single particle) / Resolution: 3.36 Å

Source
  • xenopus laevis (African clawed frog)
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsDNA BINDING PROTEIN/DNA / nucleosome / ubiquitin / histone / chromatin / DNA BINDING PROTEIN / DNA BINDING PROTEIN-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://pdbjlvh1.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