3JRV

Structure of poxvirus K7 protein in complex with RNA helicase DDX3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for targeting of human RNA helicase DDX3 by poxvirus protein K7

Oda, S.Schroder, M.Khan, A.R.

(2009) Structure 17: 1528-1537

  • DOI: https://doi.org/10.1016/j.str.2009.09.005
  • Primary Citation of Related Structures:  
    3JRV

  • PubMed Abstract: 

    Poxviruses are DNA viruses that express numerous proteins to subvert the host immune response. Vaccinia virus protein K7 adopts a Bcl-2 fold and displays structural and functional similarities to Toll-like receptor antagonist A52. Both proteins interact with IRAK2 and TRAF6 and suppress TLR-dependent NF-kappaB activation. However, unlike A52, K7 also forms a complex with RNA helicase DDX3 and antagonizes interferon-beta promoter induction. We have narrowed the K7 binding site to an N-terminal peptide motif of DDX3 ahead of its core RNA-helicase domains. The crystal structure of full-length K7 in complex with the DDX3 peptide reveals a thumblike projection of tandem phenalyalanine residues of DDX3 into a deep hydrophobic cleft. Mutagenesis of these phenylalanines abolishes the effects of DDX3 on interferon-beta promoter induction. The structure of K7-DDX3 reveals a novel binding mode by a viral Bcl-2 protein that antagonizes a key pathway in innate immunity.


  • Organizational Affiliation

    School of Biochemistry and Immunology, Trinity College, Dublin, Dublin 2, Ireland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein K7
A, B
149Vaccinia virus WRMutation(s): 0 
UniProt
Find proteins for P68466 (Vaccinia virus (strain Western Reserve))
Explore P68466 
Go to UniProtKB:  P68466
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68466
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DDX3X
C, D, E
20N/AMutation(s): 0 
EC: 3.6.1 (PDB Primary Data), 3.6.4.13 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O00571 (Homo sapiens)
Explore O00571 
Go to UniProtKB:  O00571
PHAROS:  O00571
GTEx:  ENSG00000215301 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00571
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.889α = 90
b = 69.529β = 122.17
c = 65.626γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
SHELXEmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-04-18
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Refinement description