2H0D

Structure of a Bmi-1-Ring1B Polycomb group ubiquitin ligase complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of a Bmi-1-Ring1B Polycomb Group Ubiquitin Ligase Complex.

Li, Z.Cao, R.Wang, M.Myers, M.P.Zhang, Y.Xu, R.M.

(2006) J Biol Chem 281: 20643-20649

  • DOI: https://doi.org/10.1074/jbc.M602461200
  • Primary Citation of Related Structures:  
    2H0D

  • PubMed Abstract: 

    Polycomb group proteins Bmi-1 and Ring1B are core subunits of the PRC1 complex, which plays important roles in the regulation of Hox gene expression, X-chromosome inactivation, tumorigenesis, and stem cell self-renewal. The RING finger protein Ring1B is an E3 ligase that participates in the ubiquitination of lysine 119 of histone H2A, and the binding of Bmi-1 stimulates the E3 ligase activity. We have mapped the regions of Bmi-1 and Ring1B required for efficient ubiquitin transfer and determined a 2.5-A structure of the Bmi-1-Ring1B core domain complex. The structure reveals that Ring1B "hugs" Bmi-1 through extensive RING domain contacts and its N-terminal tail wraps around Bmi-1. The two regions of interaction have a synergistic effect on the E3 ligase activity. Our analyses suggest a model where the Bmi-1-Ring1B complex stabilizes the interaction between the E2 enzyme and the nucleosomal substrate to allow efficient ubiquitin transfer.


  • Organizational Affiliation

    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B lymphoma Mo-MLV insertion region97Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P35226 (Homo sapiens)
Explore P35226 
Go to UniProtKB:  P35226
PHAROS:  P35226
GTEx:  ENSG00000168283 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35226
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin ligase protein RING2100Homo sapiensMutation(s): 0 
EC: 6.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q99496 (Homo sapiens)
Explore Q99496 
Go to UniProtKB:  Q99496
PHAROS:  Q99496
GTEx:  ENSG00000121481 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99496
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.514α = 90
b = 120.514β = 90
c = 27.209γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MADNESSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2006-05-23 
  • Deposition Author(s): Xu, R.M.

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-23
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations