3JRV

Structure of poxvirus K7 protein in complex with RNA helicase DDX3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.141 

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: 10.1016/j.str.2009.09.005

  • 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 inter ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein K7
A, B
149Vaccinia virus (strain Western Reserve)Mutation(s): 0 
Find proteins for P68466 (Vaccinia virus (strain Western Reserve))
Go to UniProtKB:  P68466
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent RNA helicase DDX3X
C, D, E
20Homo sapiensMutation(s): 0 
Gene Names: DDX3X (DBX, DDX3)
EC: 3.6.4.13
Find proteins for O00571 (Homo sapiens)
Go to Gene View: DDX3X
Go to UniProtKB:  O00571
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.141 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 90.889α = 90.00
b = 69.529β = 122.17
c = 65.626γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SHELXphasing
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data collection
PDB_EXTRACTdata extraction
SHELXEmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-09-09 
  • Released Date: 2009-11-10 
  • Deposition Author(s): Oda, S., Khan, R.A.

Revision History 

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