4HPM

PCGF1 Ub fold (RAWUL)/BCORL1 PUFD Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the Polycomb Group Protein PCGF1 in Complex with BCOR Reveals Basis for Binding Selectivity of PCGF Homologs.

Junco, S.E.Wang, R.Gaipa, J.C.Taylor, A.B.Schirf, V.Gearhart, M.D.Bardwell, V.J.Demeler, B.Hart, P.J.Kim, C.A.

(2013) Structure 21: 665-671

  • DOI: https://doi.org/10.1016/j.str.2013.02.013
  • Primary Citation of Related Structures:  
    4HPL, 4HPM

  • PubMed Abstract: 

    Polycomb-group RING finger homologs (PCGF1, PCGF2, PCGF3, PCGF4, PCGF5, and PCGF6) are critical components in the assembly of distinct Polycomb repression complex 1 (PRC1)-related complexes. Here, we identify a protein interaction domain in BCL6 corepressor, BCOR, which binds the RING finger- and WD40-associated ubiquitin-like (RAWUL) domain of PCGF1 (NSPC1) and PCGF3 but not of PCGF2 (MEL18) or PCGF4 (BMI1). Because of the selective binding, we have named this domain PCGF Ub-like fold discriminator (PUFD). The structure of BCOR PUFD bound to PCGF1 reveals that (1) PUFD binds to the same surfaces as observed for a different Polycomb group RAWUL domain and (2) the ability of PUFD to discriminate among RAWULs stems from the identity of specific residues within these interaction surfaces. These data show the molecular basis for determining the binding preference for a PCGF homolog, which ultimately helps determine the identity of the larger PRC1-like assembly.


  • Organizational Affiliation

    Department of Biochemistry and CTRC, University of Texas Health Science Center at San Antonio, MSC 7760, 7703 Floyd Curl Drive, San Antonio, TX 78229-3990, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BCL-6 corepressor-like protein 1
A, C
122Homo sapiensMutation(s): 0 
Gene Names: BCORL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q5H9F3 (Homo sapiens)
Explore Q5H9F3 
Go to UniProtKB:  Q5H9F3
PHAROS:  Q5H9F3
GTEx:  ENSG00000085185 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5H9F3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb group RING finger protein 1
B, D
93Homo sapiensMutation(s): 0 
Gene Names: NSPC1PCGF1RNF68
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BSM1 (Homo sapiens)
Explore Q9BSM1 
Go to UniProtKB:  Q9BSM1
PHAROS:  Q9BSM1
GTEx:  ENSG00000115289 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BSM1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.784α = 90
b = 65.794β = 94.73
c = 56.517γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description