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 1.3 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
  • Structures With Same Primary Citation

  • 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 regionA97Homo sapiensMutation(s): 0 
Gene Names: BMI1PCGF4RNF51
Find proteins for P35226 (Homo sapiens)
Explore P35226 
Go to UniProtKB:  P35226
NIH Common Fund Data Resources
PHAROS  P35226
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin ligase protein RING2B100Homo sapiensMutation(s): 0 
Gene Names: RNF2BAP1DINGHIPI3RING1B
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for Q99496 (Homo sapiens)
Explore Q99496 
Go to UniProtKB:  Q99496
NIH Common Fund Data Resources
PHAROS  Q99496
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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

  • 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
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description