1SFU

Crystal structure of the viral Zalpha domain bound to left-handed Z-DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A poxvirus protein forms a complex with left-handed Z-DNA: crystal structure of a Yatapoxvirus Zalpha bound to DNA.

Ha, S.C.Lokanath, N.K.Van Quyen, D.Wu, C.A.Lowenhaupt, K.Rich, A.Kim, Y.G.Kim, K.K.

(2004) Proc.Natl.Acad.Sci.USA 101: 14367-14372

  • DOI: 10.1073/pnas.0405586101

  • PubMed Abstract: 
  • A conserved feature of poxviruses is a protein, well characterized as E3L in vaccinia virus, that confers IFN resistance on the virus. This protein comprises two domains, an N-terminal Z-DNA-binding protein domain (Zalpha) and a C-terminal double-str ...

    A conserved feature of poxviruses is a protein, well characterized as E3L in vaccinia virus, that confers IFN resistance on the virus. This protein comprises two domains, an N-terminal Z-DNA-binding protein domain (Zalpha) and a C-terminal double-stranded RNA-binding domain. Both are required for pathogenicity of vaccinia virus in mice infected by intracranial injection. Here, we describe the crystal structure of the Zalpha domain from the E3L-like protein of Yaba-like disease virus, a Yatapoxvirus, in a complex with Z-DNA, solved at a 2.0-A resolution. The DNA contacting surface of Yaba-like disease virus Zalpha(E3L) closely resembles that of other structurally defined members of the Zalpha family, although some variability exists in the beta-hairpin region. In contrast to the Z-DNA-contacting surface, the nonbinding surface of members of the Zalpha family are unrelated; this surface may effect protein-specific interactions. The presence of the conserved and tailored Z-DNA-binding surface, which interacts specifically with the zigzag backbone and syn base diagnostic of the Z-form, reinforces the importance to poxvirus infection of the ability of this protein to recognize the Z-conformation.


    Organizational Affiliation

    Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
34L protein
A, B
75Yaba-like disease virusMutation(s): 0 
Gene Names: 34L
Find proteins for Q9DHS8 (Yaba-like disease virus)
Go to UniProtKB:  Q9DHS8
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*T*CP*GP*CP*GP*CP*G)-3'C,D7N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.237 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 51.203α = 90.00
b = 92.452β = 90.00
c = 48.012γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
HKL-2000data collection
SOLVEphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance