6HGC

Structure of Calypso in complex with DEUBAD of ASX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.270 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Basis for the Activation of the Deubiquitinase Calypso by the Polycomb Protein ASX.

De, I.Chittock, E.C.Grotsch, H.Miller, T.C.R.McCarthy, A.A.Muller, C.W.

(2019) Structure 27: 528-536.e4

  • DOI: https://doi.org/10.1016/j.str.2018.11.013
  • Primary Citation of Related Structures:  
    6HGC

  • PubMed Abstract: 

    Ubiquitin C-terminal hydrolase deubiquitinase BAP1 is an essential tumor suppressor involved in cell growth control, DNA damage response, and transcriptional regulation. As part of the Polycomb repression machinery, BAP1 is activated by the deubiquitinase adaptor domain of ASXL1 mediating gene repression by cleaving ubiquitin (Ub) from histone H2A in nucleosomes. The molecular mechanism of BAP1 activation by ASXL1 remains elusive, as no structures are available for either BAP1 or ASXL1. Here, we present the crystal structure of the BAP1 ortholog from Drosophila melanogaster, named Calypso, bound to its activator, ASX, homolog of ASXL1. Based on comparative structural and functional analysis, we propose a model for Ub binding by Calypso/ASX, uncover decisive structural elements responsible for ASX-mediated Calypso activation, and characterize the interaction with ubiquitinated nucleosomes. Our results give molecular insight into Calypso function and its regulation by ASX and provide the opportunity for the rational design of mechanism-based therapeutics to treat human BAP1/ASXL1-related tumors.


  • Organizational Affiliation

    European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase calypso,Ubiquitin carboxyl-terminal hydrolase calypso341Drosophila 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
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb protein AsxB [auth C]110Drosophila 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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase calypso,Ubiquitin carboxyl-terminal hydrolase calypsoC [auth B]310Drosophila 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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.268 
  • R-Value Observed: 0.270 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.505α = 90
b = 119.505β = 90
c = 408.9γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Commission277899

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-03-13
    Changes: Data collection, Database references