5CVN

WDR48 (2-580):USP46~ubiquitin ternary complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.36 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural Insights into WD-Repeat 48 Activation of Ubiquitin-Specific Protease 46.

Yin, J., Schoeffler, A.J., Wickliffe, K., Newton, K., Starovasnik, M.A., Dueber, E.C., Harris, S.F.

(2015) Structure 23: 2043-2054

  • DOI: 10.1016/j.str.2015.08.010
  • Primary Citation of Related Structures:  
    5CVL, 5CVM, 5CVN, 5CVO

  • PubMed Abstract: 

    • Protein ubiquitination patterns are an important component of cellular signaling. The WD-repeat protein WDR48 (USP1-associated factor UAF-1) stimulates activity of ubiquitin-specific proteases USP1, USP12, and USP46. To understand how WDR48 exerts its effect on the USP scaffold, we determined structures of the ternary WDR48:USP46:ubiquitin complex ...

    Protein ubiquitination patterns are an important component of cellular signaling. The WD-repeat protein WDR48 (USP1-associated factor UAF-1) stimulates activity of ubiquitin-specific proteases USP1, USP12, and USP46. To understand how WDR48 exerts its effect on the USP scaffold, we determined structures of the ternary WDR48:USP46:ubiquitin complex. WDR48 interacts with the USP46 fingers subdomain via a relatively small, highly polar surface on the top center of the WDR48 β propeller. In addition, WDR48 has a novel ancillary domain and a C-terminal SUMO-like domain encircling the USP46-bound ubiquitin. Mutation of residues involved in the WDR48:USP46 interaction abrogated both binding and deubiquitinase activity of the complex. An analogous mutation in USP1 similarly blocked WDR48-dependent activation. Our data suggest a possible mechanism of deubiquitinase stimulation via stabilization and prolonged residence time of substrate. The unprecedented mode of interaction between the USP fingers domain and the WD-repeat β propeller serves as a prototypical example for this family of deubiquitinases.

    Organizational Affiliation: 

    Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA. Electronic address: harris.seth@gene.com.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
WD repeat-containing protein 48A598Homo sapiensMutation(s): 0 
Gene Names: WDR48, KIAA1449, UAF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TAF3 (Homo sapiens)
Explore Q8TAF3 
Go to UniProtKB:  Q8TAF3
PHAROS:  Q8TAF3
GTEx:  ENSG00000114742 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TAF3
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 46B358Homo sapiensMutation(s): 0 
Gene Names: USP46
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for P62068 (Homo sapiens)
Explore P62068 
Go to UniProtKB:  P62068
PHAROS:  P62068
GTEx:  ENSG00000109189 
Entity Groups  
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UniProt GroupP62068
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-BC [auth D]96Homo sapiensMutation(s): 0 
Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
PHAROS:  P0CG47
Entity Groups  
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UniProt GroupP0CG47
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
D [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.36 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.437α = 90
b = 154.189β = 90
c = 182.854γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2015-07-27 
  • Released Date: 2015-10-07 
    • Deposition Author(s): Harris, S.F., Yin, J.

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-07
    Type: Initial release
  • Version 1.1: 2015-11-11
    Changes: Database references