4WCG | pdb_00004wcg

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.207 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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This is version 1.2 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 Biological Chem 290: 30713-30725

  • DOI: https://doi.org/10.1074/jbc.M115.679407
  • Primary Citation Related Structures: 
    4WCG

  • 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-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.

Macromolecule Content 

  • Total Structure Weight: 33.58 kDa 
  • Atom Count: 1,407 
  • Modeled Residue Count: 134 
  • Deposited Residue Count: 234 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ORF112
A, B
98Cyprinid herpesvirus 3Mutation(s): 0 
Gene Names: KHVJ122
UniProt
Find proteins for A4FTK7 (Cyprinid herpesvirus 3)
Explore A4FTK7 
Go to UniProtKB:  A4FTK7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4FTK7
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*GP*CP*GP*CP*G)-3')
C, D
19synthetic construct
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.207 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.821α = 90
b = 44.821β = 90
c = 140.082γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
XSCALEdata scaling
XSCALEdata reduction

Structure Validation

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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  (Full details and data files)

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2016-01-13
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description