› 8v1q

Electron Microscopy
2.7Å resolution

Herpes simplex virus 1 polymerase holoenzyme bound to DNA in both open/closed conformations

Released:
DOI: 10.2210/pdb8v1q/pdb
PDB entry 8v1q coloured by chain, front view.
PDB entry 8v1q coloured by chain, side view.
PDB entry 8v1q coloured by chain, top view.
Source organism: Human alphaherpesvirus 1 strain KOS
Primary publication:
Viral DNA polymerase structures reveal mechanisms of antiviral drug resistance.
Shankar S, Pan J, Yang P, Bian Y, Oroszlán G, Yu Z, Mukherjee P, Filman DJ, Hogle JM, Shekhar M, Coen DM, Abraham J
Cell (2024)
PMID: 39197451
Related structures: EMD-42887

Function and Biology Details

Reactions catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Endonucleolytic cleavage to 5'-phosphomonoester.
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-250862 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase Chain: A
Molecule details ›
Chain: A
Length: 1199 amino acids
Theoretical weight: 133.61 KDa
Source organism: Human alphaherpesvirus 1 strain KOS
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: H9E937 (Residues: 43-1235; Coverage: 97%)
Gene names: HHV1gp046, UL30
Sequence domains:
DNA polymerase processivity factor Chain: B
Molecule details ›
Chain: B
Length: 349 amino acids
Theoretical weight: 37.28 KDa
Source organism: Human alphaherpesvirus 1 strain KOS
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A181ZFK4 (Residues: 2-340; Coverage: 67%)
Gene name: P2C_00058
Sequence domains: DNA polymerase processivity factor (UL42)
Primer DNA Chain: P
Molecule details ›
Chain: P
Length: 32 nucleotides
Theoretical weight: 9.87 KDa
template DNA Chain: T
Molecule details ›
Chain: T
Length: 50 nucleotides
Theoretical weight: 15.22 KDa

Ligands and Environments

1 bound ligand:
Ligand MG 2 x MG
1 modified residue:
Ligand DOC 1 x DOC

Experiments and Validation Details

Entry percentile scores
Resolution: 2.7Å
Relevant EMDB volumes: EMD-42887
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli BL21(DE3)

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