3RPG

Bmi1/Ring1b-UbcH5c complex structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Recognition of UbcH5c and the nucleosome by the Bmi1/Ring1b ubiquitin ligase complex.

Bentley, M.L.Corn, J.E.Dong, K.C.Phung, Q.Cheung, T.K.Cochran, A.G.

(2011) EMBO J 30: 3285-3297

  • DOI: 10.1038/emboj.2011.243
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The Polycomb repressive complex 1 (PRC1) mediates gene silencing, in part by monoubiquitination of histone H2A on lysine 119 (uH2A). Bmi1 and Ring1b are critical components of PRC1 that heterodimerize via their N-terminal RING domains to form an acti ...

    The Polycomb repressive complex 1 (PRC1) mediates gene silencing, in part by monoubiquitination of histone H2A on lysine 119 (uH2A). Bmi1 and Ring1b are critical components of PRC1 that heterodimerize via their N-terminal RING domains to form an active E3 ubiquitin ligase. We have determined the crystal structure of a complex between the Bmi1/Ring1b RING-RING heterodimer and the E2 enzyme UbcH5c and find that UbcH5c interacts with Ring1b only, in a manner fairly typical of E2-E3 interactions. However, we further show that the Bmi1/Ring1b RING domains bind directly to duplex DNA through a basic surface patch unique to the Bmi1/Ring1b RING-RING dimer. Mutation of residues on this interaction surface leads to a loss of H2A ubiquitination activity. Computational modelling of the interface between Bmi1/Ring1b-UbcH5c and the nucleosome suggests that Bmi1/Ring1b interacts with both nucleosomal DNA and an acidic patch on histone H4 to achieve specific monoubiquitination of H2A. Our results point to a novel mechanism of substrate recognition, and control of product formation, by Bmi1/Ring1b.


    Organizational Affiliation

    Department of Early Discovery Biochemistry, Genentech Research and Early Development, South San Francisco, CA, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 D3
A
149Homo sapiensMutation(s): 0 
Gene Names: UBE2D3UBC5CUBCH5C
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt), 2.3.2.24 (UniProt)
Find proteins for P61077 (Homo sapiens)
Go to UniProtKB:  P61077
NIH Common Fund Data Resources
PHAROS  P61077

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polycomb complex protein BMI-1
B
117Homo sapiensMutation(s): 0 
Gene Names: BMI1PCGF4RNF51
Find proteins for P35226 (Homo sapiens)
Go to UniProtKB:  P35226
NIH Common Fund Data Resources
PHAROS  P35226

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase RING2
C
121Homo sapiensMutation(s): 0 
Gene Names: RNF2BAP1DINGHIPI3RING1B
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for Q99496 (Homo sapiens)
Go to UniProtKB:  Q99496
NIH Common Fund Data Resources
PHAROS  Q99496
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.89α = 90
b = 107.89β = 90
c = 77.572γ = 120
Software Package:
Software NamePurpose
StructureStudiodata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-17
    Type: Initial release
  • Version 1.1: 2011-08-31
    Changes: Database references