3RPG

Bmi1/Ring1b-UbcH5c complex structure

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6485 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.217 

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

  • 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: UBE2D3 (UBC5C, UBCH5C)
EC: 2.3.2.23
Find proteins for P61077 (Homo sapiens)
Go to Gene View: UBE2D3
Go to UniProtKB:  P61077
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polycomb complex protein BMI-1
B
117Homo 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: 3
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase RING2
C
121Homo 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 
B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6485 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.217 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 107.890α = 90.00
b = 107.890β = 90.00
c = 77.572γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
StructureStudiodata collection
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

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