5HSW

KSHV SOX RNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

KSHV SOX mediated host shutoff: the molecular mechanism underlying mRNA transcript processing.

Lee, H.Patschull, A.O.M.Bagneris, C.Ryan, H.Sanderson, C.M.Ebrahimi, B.Nobeli, I.Barrett, T.E.

(2017) Nucleic Acids Res. 45: 4756-4767

  • DOI: 10.1093/nar/gkw1340

  • PubMed Abstract: 
  • Onset of the lytic phase in the KSHV life cycle is accompanied by the rapid, global degradation of host (and viral) mRNA transcripts in a process termed host shutoff. Key to this destruction is the virally encoded alkaline exonuclease SOX. While SOX ...

    Onset of the lytic phase in the KSHV life cycle is accompanied by the rapid, global degradation of host (and viral) mRNA transcripts in a process termed host shutoff. Key to this destruction is the virally encoded alkaline exonuclease SOX. While SOX has been shown to possess an intrinsic RNase activity and a potential consensus sequence for endonucleolytic cleavage identified, the structures of the RNA substrates targeted remained unclear. Based on an analysis of three reported target transcripts, we were able to identify common structures and confirm that these are indeed degraded by SOX in vitro as well as predict the presence of such elements in the KSHV pre-microRNA transcript K12-2. From these studies, we were able to determine the crystal structure of SOX productively bound to a 31 nucleotide K12-2 fragment. This complex not only reveals the structural determinants required for RNA recognition and degradation but, together with biochemical and biophysical studies, reveals distinct roles for residues implicated in host shutoff. Our results further confirm that SOX and the host exoribonuclease Xrn1 act in concert to elicit the rapid degradation of mRNA substrates observed in vivo, and that the activities of the two ribonucleases are co-ordinated.


    Organizational Affiliation

    Institute for Structural and Molecular Biology, 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 MN/A
Find proteins for P88925 (Human herpesvirus 8 type M)
Go to UniProtKB:  P88925
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*CP*UP*UP*GP*AP*AP*GP*CP*AP*GP*CP*UP*UP*CP*CP*AP*G)-3')B31Human gammaherpesvirus 8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 198.200α = 90.00
b = 45.900β = 90.10
c = 67.600γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTERrefinement
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-01-26 
  • Released Date: 2017-02-01 
  • Deposition Author(s): Barrett, T.E.

Funding OrganizationCountryGrant Number
Wellcome TrustUnited KingdomWT083336MA

Revision History 

  • Version 1.0: 2017-02-01
    Type: Initial release
  • Version 1.1: 2017-02-08
    Type: Database references
  • Version 1.2: 2017-02-15
    Type: Database references
  • Version 1.3: 2017-05-17
    Type: Database references