› 4iox

X-ray diffraction
2.46Å resolution

The structure of the herpes simplex virus DNA-packaging motor pUL15 C-terminal nuclease domain provides insights into cleavage of concatemeric viral genome precursors

Released:
DOI: 10.2210/pdb4iox/pdb
PDB entry 4iox coloured by chain, front view.
PDB entry 4iox coloured by chain, side view.
PDB entry 4iox coloured by chain, top view.
Source organism: Human alphaherpesvirus 1
Primary publication:
The structure of the herpes simplex virus DNA-packaging terminase pUL15 nuclease domain suggests an evolutionary lineage among eukaryotic and prokaryotic viruses.
Selvarajan Sigamani S, Zhao H, Kamau YN, Baines JD, Tang L
J Virol 87 7140-8 (2013)
PMID: 23596306

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-137583 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Tripartite terminase subunit 3 Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 286 amino acids
Theoretical weight: 30.92 KDa
Source organism: Human alphaherpesvirus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: P04295 (Residues: 471-735; Coverage: 36%)
Gene names: TRM3, UL15
Sequence domains: Probable DNA packing protein, C-terminus
Structure domains: Nucleotidyltransferase; domain 5
peptide Chain: D
Molecule details ›
Chain: D
Length: 6 amino acids
Theoretical weight: 529 Da
Source organism: Human alphaherpesvirus 1
Expression system: Escherichia coli

Ligands and Environments

4 bound ligands:
Ligand PGE 1 x PGE
Ligand PEG 1 x PEG
Ligand PG4 1 x PG4
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: P43212
Unit cell:
a: 96.944Å b: 96.944Å c: 194.034Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.205 0.203 0.247
Expression system: Escherichia coli

Quick links

Citations

14 review citations

Origins and evolution of viruses of eukaryotes: The ultimate modularity.
Koonin et al. (2015)
13 more

8 mentions without citation

Development of Potent Antiviral Drugs Inspired by Viral Hexameric DNA-Packaging Motors with Revolving Mechanism.
Pi et al. (2016)
7 more