4LB6

Crystal structure of PKZ Zalpha in complex with ds(CG)6 (tetragonal form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for Z-DNA binding and stabilization by the zebrafish Z-DNA dependent protein kinase PKZ.

de Rosa, M.Zacarias, S.Athanasiadis, A.

(2013) Nucleic Acids Res. 41: 9924-9933

  • DOI: 10.1093/nar/gkt743
  • Primary Citation of Related Structures:  4LB5

  • PubMed Abstract: 
  • The RNA-dependent protein kinase PKR plays a central role in the antiviral defense of vertebrates by shutting down protein translation upon detection of viral dsRNA in the cytoplasm. In some teleost fish, PKZ, a homolog of PKR, performs the same func ...

    The RNA-dependent protein kinase PKR plays a central role in the antiviral defense of vertebrates by shutting down protein translation upon detection of viral dsRNA in the cytoplasm. In some teleost fish, PKZ, a homolog of PKR, performs the same function, but surprisingly, instead of dsRNA binding domains, it harbors two Z-DNA/Z-RNA-binding domains belonging to the Zalpha domain family. Zalpha domains have also been found in other proteins, which have key roles in the regulation of interferon responses such as ADAR1 and DNA-dependent activator of IFN-regulatory factors (DAI) and in viral proteins involved in immune response evasion such as the poxviral E3L and the Cyprinid Herpesvirus 3 ORF112. The underlying mechanism of nucleic acids binding and stabilization by Zalpha domains is still unclear. Here, we present two crystal structures of the zebrafish PKZ Zalpha domain (DrZalpha(PKZ)) in alternatively organized complexes with a (CG)6 DNA oligonucleotide at 2 and 1.8 Å resolution. These structures reveal novel aspects of the Zalpha interaction with DNA, and they give insights on the arrangement of multiple Zalpha domains on DNA helices longer than the minimal binding site.


    Organizational Affiliation

    Instituto Gulbenkian de Ciência, Rua Quinta Grande 6, 2780-156 Oeiras, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein kinase containing Z-DNA binding domains
B
72Danio rerioGene Names: pkz
Find proteins for Q5NE14 (Danio rerio)
Go to UniProtKB:  Q5NE14
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*TP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3'C13N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.181 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 110.910α = 90.00
b = 110.910β = 90.00
c = 43.140γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
DNAdata collection
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2013-12-04
    Type: Database references