4S3O

PCGF5-RING1B-UbcH5c complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

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
  • Primary Citation of Related Structures:  
    4S3O

  • 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 subunit wh ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 D3 AD148Homo 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)
Explore P61077 
Go to UniProtKB:  P61077
NIH Common Fund Data Resources
PHAROS:  P61077
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RING2 BE118Homo 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
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PHAROS:  Q99496
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Polycomb group RING finger protein 5 CF117Homo sapiensMutation(s): 0 
Gene Names: PCGF5RNF159
Find proteins for Q86SE9 (Homo sapiens)
Explore Q86SE9 
Go to UniProtKB:  Q86SE9
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PHAROS:  Q86SE9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.392α = 90
b = 105.285β = 90
c = 132.417γ = 90
Software Package:
Software NamePurpose
BOSdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

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