› 3pov

X-ray diffraction
2.5Å resolution

Crystal structure of a SOX-DNA complex

Released:
DOI: 10.2210/pdb3pov/pdb
PDB entry 3pov coloured by chain, front view.
PDB entry 3pov coloured by chain, side view.
PDB entry 3pov coloured by chain, top view.
Source organism: Human herpesvirus 8 type M
Primary publication:
Crystal structure of a KSHV-SOX-DNA complex: insights into the molecular mechanisms underlying DNase activity and host shutoff.
Bagnéris C, Briggs LC, Savva R, Ebrahimi B, Barrett TE
Nucleic Acids Res 39 5744-56 (2011)
PMID: 21421561

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116707 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
ORF 37 Chain: A
Molecule details ›
Chain: A
Length: 488 amino acids
Theoretical weight: 55.3 KDa
Source organism: Human herpesvirus 8 type M
Expression system: Escherichia coli
UniProt:
  • Canonical: P88925 (Residues: 1-486; Coverage: 100%)
Sequence domains: Viral alkaline exonuclease
Structure domains: Herpesvirus alkaline exonuclease, N-terminal domain
DNA (5'-D(*GP*GP*GP*AP*TP*CP*CP*TP*CP*CP*CP*AP*GP*TP*CP*GP*AP*CP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 19 nucleotides
Theoretical weight: 5.77 KDa
Source organism: Human herpesvirus 8 type M
Expression system: Not provided
DNA (5'-D(*GP*GP*TP*CP*GP*AP*CP*TP*AP*GP*GP*AP*GP*GP*AP*TP*CP*CP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 19 nucleotides
Theoretical weight: 5.87 KDa
Source organism: Human herpesvirus 8 type M
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand FMT 1 x FMT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P212121
Unit cell:
a: 54.52Å b: 67.66Å c: 174.56Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.206 0.264
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

9 review citations

Shutoff of Host Gene Expression in Influenza A Virus and Herpesviruses: Similar Mechanisms and Common Themes.
Rivas et al. (2016)
8 more

6 mentions without citation

Structure and mechanism of the Red recombination system of bacteriophage λ.
Caldwell et al. (2019)
5 more