Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.42 kDa 
• Atom Count: 734 
• Modelled Residue Count: 69 
• Deposited Residue Count: 85 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

4LB6

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

• PDB DOI: 10.2210/pdb4LB6/pdb
• NDB: NA2567

• Classification: TRANSFERASE/DNA
• Organism(s): Danio rerio
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-06-20 Released: 2013-09-18 
• Deposition Author(s): De Rosa, M., Zacarias, S., Athanasiadis, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.212 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 

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

• PubMed: 23975196 
• DOI: 10.1093/nar/gkt743
• Primary Citation of Related Structures:  
  4LB5, 4LB6


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein kinase containing Z-DNA binding domains	A [auth B]	72	Danio rerio	Mutation(s): 0  Gene Names: pkz EC: 2.7.11.1
UniProt
Find proteins for Q5NE14 (Danio rerio) Explore Q5NE14  Go to UniProtKB:  Q5NE14

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3'	B [auth C]	13	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.212 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.91	α = 90
b = 110.91	β = 90
c = 43.14	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-06-20 
• Released Date: 2013-09-18 
Deposition Author(s): De Rosa, M., Zacarias, S., Athanasiadis, A.

Revision History  

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