5CVL

WDR48 (UAF-1), residues 2-580


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.186 

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:  

  • 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 it ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
WD repeat-containing protein 48
A
598Homo sapiensMutation(s): 0 
Gene Names: WDR48 (KIAA1449, UAF1)
Find proteins for Q8TAF3 (Homo sapiens)
Go to Gene View: WDR48
Go to UniProtKB:  Q8TAF3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
AU
Query on AU

Download SDF File 
Download CCD File 
A
GOLD ION
Au
ZBKIUFWVEIBQRT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.186 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 139.520α = 90.00
b = 139.520β = 90.00
c = 235.109γ = 90.00
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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