3POV | pdb_00003pov

Crystal structure of a SOX-DNA complex

• PDB DOI: https://doi.org/10.2210/pdb3POV/pdb
• NAKB: 3POV

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Human herpesvirus 8 type M
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-11-23 Released: 2011-09-21 
• Deposition Author(s): Bagneris, C., Barrett, T.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.264 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

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

• PubMed: 21421561 
• DOI: https://doi.org/10.1093/nar/gkr111
• Primary Citation 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.

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Organizational Affiliation: 
• Institute of Structural and Molecular Biology, Crystallography, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX , 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: 67.03 kDa 
• Atom Count: 4,373 
• Modeled Residue Count: 483 
• Deposited Residue Count: 526 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF 37	A	488	Human herpesvirus 8 type M	Mutation(s): 0  Gene Names: orf37
UniProt
Find proteins for P88925 (Human herpesvirus 8 type M) Explore P88925  Go to UniProtKB:  P88925

Entity ID: 2
Molecule	Chains	Length	Organism	Image
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]	19	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
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]	19	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	F [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
MG	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.264 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.52	α = 90
b = 67.66	β = 90
c = 174.56	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
MOLREP	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-21 
Deposition Author(s): Bagneris, C., Barrett, T.E.

Revision History  

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