2H0D

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1074/jbc.M602461200

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
B lymphoma Mo-MLV insertion region
A
97Homo sapiensMutation(s): 0 
Gene Names: BMI1 (PCGF4, RNF51)
Find proteins for P35226 (Homo sapiens)
Go to Gene View: BMI1
Go to UniProtKB:  P35226
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin ligase protein RING2
B
100Homo sapiensMutation(s): 0 
Gene Names: RNF2 (BAP1, DING, HIPI3, RING1B)
EC: 2.3.2.27
Find proteins for Q99496 (Homo sapiens)
Go to Gene View: RNF2
Go to UniProtKB:  Q99496
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.210 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 120.514α = 90.00
b = 120.514β = 90.00
c = 27.209γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SOLVEphasing
SCALEPACKdata scaling
MADNESSdata reduction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2006-05-14 
  • Released Date: 2006-05-23 
  • Deposition Author(s): Xu, R.M.

Revision History 

  • Version 1.0: 2006-05-23
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description