6CGA

Structure of the PR-DUB complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A bidentate Polycomb Repressive-Deubiquitinase complex is required for efficient activity on nucleosomes.

Foglizzo, M.Middleton, A.J.Burgess, A.E.Crowther, J.M.Dobson, R.C.J.Murphy, J.M.Day, C.L.Mace, P.D.

(2018) Nat Commun 9: 3932-3932

  • DOI: https://doi.org/10.1038/s41467-018-06186-1
  • Primary Citation of Related Structures:  
    6CGA

  • PubMed Abstract: 

    Attachment of ubiquitin to lysine 119 of Histone 2A (H2AK119Ub) is an epigenetic mark characteristic of repressed developmental genes, which is removed by the Polycomb Repressive-Deubiquitinase (PR-DUB) complex. Here we report the crystal structure of the Drosophila PR-DUB, revealing that the deubiquitinase Calypso and its activating partner ASX form a 2:2 complex. The bidentate Calypso-ASX complex is generated by dimerisation of two activated Calypso proteins through their coiled-coil regions. Disrupting the Calypso dimer interface does not affect inherent catalytic activity, but inhibits removal of H2AK119Ub as a consequence of impaired recruitment to nucleosomes. Mutating the equivalent surface on the human counterpart, BAP1, also compromises activity on nucleosomes. Together, this suggests that high local concentrations drive assembly of bidentate PR-DUB complexes on chromatin-providing a mechanistic basis for enhanced PR-DUB activity at specific genomic foci, and the impact of distinct classes of PR-DUB mutations in tumorigenesis.


  • Organizational Affiliation

    Biochemistry Department, School of Biomedical Sciences, University of Otago, P.O. Box 56, 710, Cumberland St., Dunedin, 9054, New Zealand.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase calypso
A, C
365Drosophila melanogasterMutation(s): 0 
Gene Names: calypsoCG8445
EC: 3.4.19.12
UniProt
Find proteins for Q7K5N4 (Drosophila melanogaster)
Explore Q7K5N4 
Go to UniProtKB:  Q7K5N4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7K5N4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb protein Asx
B, D
134Drosophila melanogasterMutation(s): 0 
Gene Names: AsxCG8787
UniProt
Find proteins for Q9V727 (Drosophila melanogaster)
Explore Q9V727 
Go to UniProtKB:  Q9V727
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9V727
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.17α = 90
b = 65.63β = 114.35
c = 162.76γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-03
    Type: Initial release
  • Version 1.1: 2018-10-10
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-15
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description