4WCG

The binding mode of Cyprinid Herpesvirus3 ORF112-Zalpha to Z-DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Structure of the Cyprinid herpesvirus 3 ORF112-Z alpha Z-DNA Complex Reveals a Mechanism of Nucleic Acids Recognition Conserved with E3L, a Poxvirus Inhibitor of Interferon Response.

Kus, K.Rakus, K.Boutier, M.Tsigkri, T.Gabriel, L.Vanderplasschen, A.Athanasiadis, A.

(2015) J.Biol.Chem. 290: 30713-30725

  • DOI: 10.1074/jbc.M115.679407

  • PubMed Abstract: 
  • In vertebrate species, the innate immune system down-regulates protein translation in response to viral infection through the action of the double-stranded RNA (dsRNA)-activated protein kinase (PKR). In some teleost species another protein kinase, Z- ...

    In vertebrate species, the innate immune system down-regulates protein translation in response to viral infection through the action of the double-stranded RNA (dsRNA)-activated protein kinase (PKR). In some teleost species another protein kinase, Z-DNA-dependent protein kinase (PKZ), plays a similar role but instead of dsRNA binding domains, PKZ has Zα domains. These domains recognize the left-handed conformer of dsDNA and dsRNA known as Z-DNA/Z-RNA. Cyprinid herpesvirus 3 infects common and koi carp, which have PKZ, and encodes the ORF112 protein that itself bears a Zα domain, a putative competitive inhibitor of PKZ. Here we present the crystal structure of ORF112-Zα in complex with an 18-bp CpG DNA repeat, at 1.5 Å. We demonstrate that the bound DNA is in the left-handed conformation and identify key interactions for the specificity of ORF112. Localization of ORF112 protein in stress granules induced in Cyprinid herpesvirus 3-infected fish cells suggests a functional behavior similar to that of Zα domains of the interferon-regulated, nucleic acid surveillance proteins ADAR1 and DAI.


    Organizational Affiliation

    From the Instituto Gulbenkian de Ciência, 2781-156, Oeiras, Portugal and.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ORF112
A, B
98Cyprinid herpesvirus 3Mutation(s): 0 
Gene Names: ORF112
Find proteins for A4FTK7 (Cyprinid herpesvirus 3)
Go to UniProtKB:  A4FTK7
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*CP*GP*CP*GP*CP*G)-3')C,D19synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.178 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 44.821α = 90.00
b = 44.821β = 90.00
c = 140.082γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
XSCALEdata reduction
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Foundation for Science and Technology (FCT)PortugalSFRH/BD/51626/2011
Foundation for Science and Technology (FCT)PortugalPTDC/BIA-PRO/112962/2009

Revision History 

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2016-01-13
    Type: Database references