[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

TitleThe internal interaction in RBBP5 regulates assembly and activity of MLL1 methyltransferase complex.
Journal, issue, pagesNucleic Acids Res, Vol. 47, Issue 19, Page 10426-10438, Year 2019
Publish dateNov 4, 2019
AuthorsJianming Han / Tingting Li / Yanjing Li / Muchun Li / Xiaoman Wang / Chao Peng / Chen Su / Na Li / Yiwen Li / Ying Xu / Yong Chen /
PubMed AbstractThe Mixed Lineage Leukemia protein 1 (MLL1) plays an essential role in the maintenance of the histone H3 lysine 4 (H3K4) methylation status for gene expression during differentiation and development. ...The Mixed Lineage Leukemia protein 1 (MLL1) plays an essential role in the maintenance of the histone H3 lysine 4 (H3K4) methylation status for gene expression during differentiation and development. The methyltransferase activity of MLL1 is regulated by three conserved core subunits, WDR5, RBBP5 and ASH2L. Here, we determined the structure of human RBBP5 and demonstrated its role in the assembly and regulation of the MLL1 complex. We identified an internal interaction between the WD40 propeller and the C-terminal distal region in RBBP5, which assisted the maintenance of the compact conformation of the MLL1 complex. We also discovered a vertebrate-specific motif in the C-terminal distal region of RBBP5 that contributed to nucleosome recognition and methylation of nucleosomes by the MLL1 complex. Our results provide new insights into functional conservation and evolutionary plasticity of the scaffold protein RBBP5 in the regulation of KMT2-family methyltransferase complexes.
External linksNucleic Acids Res / PubMed:31544921 / PubMed Central
MethodsSAS (X-ray synchrotron) / X-ray diffraction
Resolution1.801 Å
Structure data

SASDGD4: Mixed lineage leukemia protein-1 complex, MLL1-WDR5-ASH2L-RBBP5(2-381)
Method: SAXS/SANS

SASDGE4: Mixed lineage leukemia protein-1 complex, MLL1-WDR5-ASH2L-RBBP5(2-480)
Method: SAXS/SANS

SASDGF4: Mixed lineage leukemia protein-1 complex, MLL1-WDR5-ASH2L-RBBP5(2-480)L399A/L400A/I457A/L459A
Method: SAXS/SANS

SASDGG4: Mixed lineage leukemia protein-1 complex, MLL1-WDR5-ASH2L-RBBP5(2-538)
Method: SAXS/SANS

PDB-6km7:
The structural basis for the internal interaction in RBBP5
Method: X-RAY DIFFRACTION / Resolution: 1.801 Å

Chemicals

ChemComp-SO4:
SULFATE ION / Sulfate

ChemComp-2PE:
NONAETHYLENE GLYCOL / precipitant*YM / Polyethylene glycol

ChemComp-P6G:
HEXAETHYLENE GLYCOL / precipitant*YM / Polyethylene glycol

ChemComp-PG4:
TETRAETHYLENE GLYCOL / precipitant*YM / Polyethylene glycol

ChemComp-HOH:
WATER / Water

Source
  • homo sapiens (human)
KeywordsPROTEIN BINDING / Histone methyltransferase / MLL1 complex / RBBP5 / histone methylation / epigenetics

+
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