3I8C

Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR21A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A promiscuous alpha-helical motif anchors viral hijackers and substrate receptors to the CUL4-DDB1 ubiquitin ligase machinery.

Li, T.Robert, E.I.van Breugel, P.C.Strubin, M.Zheng, N.

(2010) Nat.Struct.Mol.Biol. 17: 105-111

  • DOI: 10.1038/nsmb.1719
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The cullin 4-DNA-damage-binding protein 1 (CUL4-DDB1) ubiquitin ligase machinery regulates diverse cellular functions and can be subverted by pathogenic viruses. Here we report the crystal structure of DDB1 in complex with a central fragment of hepat ...

    The cullin 4-DNA-damage-binding protein 1 (CUL4-DDB1) ubiquitin ligase machinery regulates diverse cellular functions and can be subverted by pathogenic viruses. Here we report the crystal structure of DDB1 in complex with a central fragment of hepatitis B virus X protein (HBx), whose DDB1-binding activity is important for viral infection. The structure reveals that HBx binds DDB1 through an alpha-helical motif, which is also found in the unrelated paramyxovirus SV5-V protein despite their sequence divergence. Our structure-based functional analysis suggests that, like SV5-V, HBx captures DDB1 to redirect the ubiquitin ligase activity of the CUL4-DDB1 E3 ligase. We also identify the alpha-helical motif shared by these viral proteins in the cellular substrate-recruiting subunits of the E3 complex, the DDB1-CUL4-associated factors (DCAFs) that are functionally mimicked by the viral hijackers. Together, our studies reveal a common yet promiscuous structural element that is important for the assembly of cellular and virally hijacked CUL4-DDB1 E3 complexes.


    Organizational Affiliation

    Department of Pharmacology, University of Washington, Seattle, Washington, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA damage-binding protein 1
A
1143Homo sapiensMutation(s): 0 
Gene Names: DDB1 (XAP1)
Find proteins for Q16531 (Homo sapiens)
Go to Gene View: DDB1
Go to UniProtKB:  Q16531
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
WD repeat-containing protein 21A
B
13Homo sapiensMutation(s): 0 
Gene Names: DCAF4 (WDR21, WDR21A)
Find proteins for Q8WV16 (Homo sapiens)
Go to Gene View: DCAF4
Go to UniProtKB:  Q8WV16
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.251 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 64.107α = 90.00
b = 134.468β = 90.00
c = 183.595γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction
PHASERphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance