[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

TitleH2B Lys34 Ubiquitination Induces Nucleosome Distortion to Stimulate Dot1L Activity.
Journal, issue, pagesNat Chem Biol, Vol. 18, Issue 9, Page 972-980, Year 2022
Publish dateJun 23, 2022
AuthorsHuasong Ai / Maoshen Sun / Aijun Liu / Zixian Sun / Tingting Liu / Lin Cao / Lujun Liang / Qian Qu / Zichen Li / Zhiheng Deng / Zebin Tong / Guochao Chu / Xiaolin Tian / Haiteng Deng / Suwen Zhao / Jia-Bin Li / Zhiyong Lou / Lei Liu /
PubMed AbstractUbiquitination-dependent histone crosstalk plays critical roles in chromatin-associated processes and is highly associated with human diseases. Mechanism studies of the crosstalk have been of the ...Ubiquitination-dependent histone crosstalk plays critical roles in chromatin-associated processes and is highly associated with human diseases. Mechanism studies of the crosstalk have been of the central focus. Here our study on the crosstalk between H2BK34ub and Dot1L-catalyzed H3K79me suggests a novel mechanism of ubiquitination-induced nucleosome distortion to stimulate the activity of an enzyme. We determined the cryo-electron microscopy structures of Dot1L-H2BK34ub nucleosome complex and the H2BK34ub nucleosome alone. The structures reveal that H2BK34ub induces an almost identical orientation and binding pattern of Dot1L on nucleosome as H2BK120ub, which positions Dot1L for the productive conformation through direct ubiquitin-enzyme contacts. However, H2BK34-anchored ubiquitin does not directly interact with Dot1L as occurs in the case of H2BK120ub, but rather induces DNA and histone distortion around the modified site. Our findings establish the structural framework for understanding the H2BK34ub-H3K79me trans-crosstalk and highlight the diversity of mechanisms for histone ubiquitination to activate chromatin-modifying enzymes.
External linksNat Chem Biol / PubMed:35739357
MethodsEM (single particle)
Resolution2.57 - 3.48 Å
Structure data

33126

7xcr

EMDB-33126, PDB-7xcr:
Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 1:1 complex
Method: EM (single particle) / Resolution: 2.57 Å

33127

7xct

EMDB-33127, PDB-7xct:
Cryo-EM structure of Dot1L and H2BK34ub-H3K79Nle nucleosome 2:1 complex
Method: EM (single particle) / Resolution: 2.72 Å

EMDB-33128: cryo-EM map of Dot1L and H2BK34ub-H3K79Nle nucleosome complex containing addition map (1:1)
Method: EM (single particle) / Resolution: 2.97 Å

33131

7xd0

EMDB-33131, PDB-7xd0:
cryo-EM structure of H2BK34ub nucleosome
Method: EM (single particle) / Resolution: 3.48 Å

33132

7xd1

EMDB-33132, PDB-7xd1:
cryo-EM structure of unmodified nucleosome
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-33139: cryo-EM map of Dot1L and H3K79Nle nucleosome complex (active state)
Method: EM (single particle) / Resolution: 3.06 Å

EMDB-33141: cryo-EM map of Dot1L and H3K79Nle nucleosome complex (inactive state)
Method: EM (single particle) / Resolution: 3.27 Å

Chemicals

ChemComp-SAM:
S-ADENOSYLMETHIONINE / S-Adenosyl methionine

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsNUCLEAR PROTEIN / Complex / Dot1L / H2BK34ub / Nucleosome / H2BK34ub nucleosome / unmodified nucleosome

+
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