3POV

Crystal structure of a SOX-DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1093/nar/gkr111

  • 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 acti ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ORF 37
A
488Human herpesvirus 8 type MMutation(s): 0 
EC: 3.1.-.-
Find proteins for P88925 (Human herpesvirus 8 type M)
Go to UniProtKB:  P88925
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*GP*AP*TP*CP*CP*TP*CP*CP*CP*AP*GP*TP*CP*GP*AP*CP*C)-3')C19N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*TP*CP*GP*AP*CP*TP*AP*GP*GP*AP*GP*GP*AP*TP*CP*CP*C)-3')D19N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

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Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.520α = 90.00
b = 67.660β = 90.00
c = 174.560γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
DNAdata collection
PHENIXrefinement
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-21
    Type: Initial release