2B5L | pdb_00002b5l

Crystal Structure of DDB1 In Complex with Simian Virus 5 V Protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.299 (Depositor), 0.293 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2B5L

This is version 1.4 of the entry. See complete history

Literature

Structure of DDB1 in complex with a paramyxovirus V protein: viral hijack of a propeller cluster in ubiquitin ligase.

Li, T.Chen, X.Garbutt, K.C.Zhou, P.Zheng, N.

(2006) Cell 124: 105-117

  • DOI: https://doi.org/10.1016/j.cell.2005.10.033
  • Primary Citation Related Structures: 
    2B5L, 2B5M, 2B5N

  • PubMed Abstract: 

    The DDB1-Cul4A ubiquitin ligase complex promotes protein ubiquitination in diverse cellular functions and is reprogrammed by the V proteins of paramyxoviruses to degrade STATs and block interferon signaling. Here we report the crystal structures of DDB1 alone and in complex with the simian virus 5 V protein. The DDB1 structure reveals an intertwined three-propeller cluster, which contains two tightly coupled beta propellers with a large pocket in between and a third beta propeller flexibly attached on the side. The rigid double-propeller fold of DDB1 is targeted by the viral V protein, which inserts an entire helix into the double-propeller pocket, whereas the third propeller domain docks DDB1 to the N terminus of the Cul4A scaffold. Together, these results not only provide structural insights into how the virus hijacks the DDB1-Cul4A ubiquitin ligase but also establish a structural framework for understanding the multiple functions of DDB1 in the uniquely assembled cullin-RING E3 machinery.


  • Organizational Affiliation
    • Department of Pharmacology, University of Washington, Seattle, WA 98195, USA.

Macromolecule Content 

  • Total Structure Weight: 302.43 kDa 
  • Atom Count: 20,399 
  • Modeled Residue Count: 2,615 
  • Deposited Residue Count: 2,724 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
damage-specific DNA binding protein 1
A, B
1,140Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens)
Explore Q16531 
Go to UniProtKB:  Q16531
PHAROS:  Q16531
GTEx:  ENSG00000167986 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16531
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nonstructural protein V
C, D
222Mammalian orthorubulavirus 5Mutation(s): 0 
Gene Names: P/V
UniProt
Find proteins for P11207 (Parainfluenza virus 5 (strain W3))
Explore P11207 
Go to UniProtKB:  P11207
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11207
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.299 (Depositor), 0.293 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.758α = 90
b = 240.792β = 101.787
c = 117.177γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-28
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary