› 8oja

Electron Microscopy
1.87Å resolution

HSV-1 DNA polymerase-processivity factor complex in exonuclease state

Released:
DOI: 10.2210/pdb8oja/pdb
PDB entry 8oja coloured by chain, front view.
PDB entry 8oja coloured by chain, side view.
PDB entry 8oja coloured by chain, top view.
Source organism: Human alphaherpesvirus 1 strain KOS
Primary publication:
Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM.
Gustavsson E, Grünewald K, Elias P, Hällberg BM
OpenAccess logo Nucleic Acids Res (2024)
PMID: 38806233
Related structures: EMD-16909

Function and Biology Details

Reactions catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Endonucleolytic cleavage to 5'-phosphomonoester.
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-242534 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase catalytic subunit Chain: A
Molecule details ›
Chain: A
Length: 1235 amino acids
Theoretical weight: 136.68 KDa
Source organism: Human alphaherpesvirus 1 strain KOS
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P04293 (Residues: 1-1235; Coverage: 100%)
Gene name: UL30
Sequence domains:
DNA polymerase processivity factor Chain: B
Molecule details ›
Chain: B
Length: 488 amino acids
Theoretical weight: 51.21 KDa
Source organism: Human alphaherpesvirus 1 strain KOS
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P10226 (Residues: 1-488; Coverage: 100%)
Gene name: UL42
Sequence domains: DNA polymerase processivity factor (UL42)
DNA (47-MER) Chain: C
Molecule details ›
Chain: C
Length: 47 nucleotides
Theoretical weight: 14.26 KDa
DNA (68-MER) Chain: D
Molecule details ›
Chain: D
Length: 68 nucleotides
Theoretical weight: 21.23 KDa

Ligands and Environments

1 bound ligand:
Ligand CA 2 x CA
1 modified residue:
Ligand AS 1 x AS

Experiments and Validation Details

Entry percentile scores
Resolution: 1.87Å
Relevant EMDB volumes: EMD-16909
Expression system: Spodoptera frugiperda

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