5HSW | pdb_00005hsw

KSHV SOX RNA complex

• PDB DOI: https://doi.org/10.2210/pdb5HSW/pdb
• NAKB: 5HSW

• Classification: HYDROLASE
• Organism(s): Human herpesvirus 8 type M, Human gammaherpesvirus 8
• Expression System: Escherichia coli
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.262 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

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

• PubMed: 28132029 
• DOI: https://doi.org/10.1093/nar/gkw1340
• Primary Citation Related Structures: 
  5HSW


• 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 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.

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Organizational Affiliation: 
• Institute for Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK.
Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK.
Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool, L69 3BX, UK.
Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 65.24 kDa 
• Atom Count: 3,625 
• Modeled Residue Count: 446 
• Deposited Residue Count: 519 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF 37	A	488	Human herpesvirus 8 type M	Mutation(s): 1
UniProt
Find proteins for P88925 (Human herpesvirus 8 type M) Explore P88925  Go to UniProtKB:  P88925

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*CP*UP*UP*GP*AP*AP*GP*CP*AP*GP*CP*UP*UP*CP*CP*AP*G)-3')	B	31	Human gammaherpesvirus 8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.262 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 198.2	α = 90
b = 45.9	β = 90.1
c = 67.6	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	WT083336MA

Revision History  

• Version 1.0: 2017-02-01
  Type: Initial release
  
• Version 1.1: 2017-02-08
  Changes: Database references
• Version 1.2: 2017-02-15
  Changes: Database references
• Version 1.3: 2017-05-17
  Changes: Database references
• Version 1.4: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-11-13
  Changes: Structure summary