3POV

Crystal structure of a SOX-DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

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This is version 1.1 of the entry. See complete history


Literature

Crystal structure of a KSHV-SOX-DNA complex: insights into the molecular mechanisms underlying DNase activity and host shutoff

Bagneris, C.Briggs, L.C.Savva, R.Ebrahimi, B.Barrett, T.E.

(2011) Nucleic Acids Res 39: 5744-5756

  • DOI: https://doi.org/10.1093/nar/gkr111
  • Primary Citation of Related Structures:  
    3POV

  • PubMed Abstract: 

    The early lytic phase of Kaposi's sarcoma herpesvirus infection is characterized by viral replication and the global degradation (shutoff) of host mRNA. Key to both activities is the virally encoded alkaline exonuclease KSHV SOX. While the DNase activity of KSHV SOX is required for the resolution of viral genomic DNA as a precursor to encapsidation, its exact involvement in host shutoff remains to be determined. We present the first crystal structure of a KSHV SOX-DNA complex that has illuminated the catalytic mechanism underpinning both its endo and exonuclease activities. We further illustrate that KSHV SOX, similar to its Epstein-Barr virus homologue, has an intrinsic RNase activity in vitro that although an element of host shutoff, cannot solely account for the phenomenon.


  • Organizational Affiliation

    Institute of Structural and Molecular Biology, Crystallography, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX , UK.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ORF 37488Human herpesvirus 8 type MMutation(s): 0 
Gene Names: orf37
UniProt
Find proteins for P88925 (Human herpesvirus 8 type M)
Explore P88925 
Go to UniProtKB:  P88925
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP88925
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*GP*GP*AP*TP*CP*CP*TP*CP*CP*CP*AP*GP*TP*CP*GP*AP*CP*C)-3')B [auth C]19N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*GP*TP*CP*GP*AP*CP*TP*AP*GP*GP*AP*GP*GP*AP*TP*CP*CP*C)-3')C [auth D]19N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.52α = 90
b = 67.66β = 90
c = 174.56γ = 90
Software Package:
Software NamePurpose
DNAdata collection
MOLREPphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description