4S3O

PCGF5-RING1B-UbcH5c complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

BMI1-RING1B is an autoinhibited RING E3 ubiquitin ligase.

Taherbhoy, A.M.Huang, O.W.Cochran, A.G.

(2015) Nat Commun 6: 7621-7621

  • DOI: 10.1038/ncomms8621

  • PubMed Abstract: 
  • Polycomb repressive complex 1 (PRC1) is required for ubiquitination of histone H2A lysine 119, an epigenetic mark associated with repression of genes important in developmental regulation. The E3 ligase activity of PRC1 resides in the RING1A/B subuni ...

    Polycomb repressive complex 1 (PRC1) is required for ubiquitination of histone H2A lysine 119, an epigenetic mark associated with repression of genes important in developmental regulation. The E3 ligase activity of PRC1 resides in the RING1A/B subunit when paired with one of six PCGF partners. The best known of these is the oncogene BMI1/PCGF4. We find that canonical PRC1 E3 ligases such as PCGF4-RING1B have intrinsically very low enzymatic activity compared with non-canonical PRC1 RING dimers. The structure of a high-activity variant in complex with E2 (PCGF5-RING1B-UbcH5c) reveals only subtle differences from an earlier PCGF4 complex structure. However, two charged residues present in the modelled interface with E2-conjugated ubiquitin prove critical: in BMI1/PCGF4, these residues form a salt bridge that may limit efficient ubiquitin transfer. The intrinsically low activity of the PCGF4-RING1B heterodimer is offset by a relatively favourable interaction with nucleosome substrates, resulting in an efficient site-specific monoubiquitination.


    Organizational Affiliation

    Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 D3
A, D
148Homo 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
E3 ubiquitin-protein ligase RING2
B, E
118Homo 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
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Polycomb group RING finger protein 5
C, F
117Homo sapiensMutation(s): 0 
Gene Names: PCGF5 (RNF159)
Find proteins for Q86SE9 (Homo sapiens)
Go to Gene View: PCGF5
Go to UniProtKB:  Q86SE9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.392α = 90.00
b = 105.285β = 90.00
c = 132.417γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PHASERphasing
BOSdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-07-22
    Type: Database references