› 9f6d

Electron Microscopy
3.6Å resolution

Human DNA polymerase epsilon bound to DNA and PCNA (open conformation)

Released:
DOI: 10.2210/pdb9f6d/pdb
PDB entry 9f6d coloured by chain, front view.
PDB entry 9f6d coloured by chain, side view.
PDB entry 9f6d coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for processive daughter-strand synthesis and proofreading by the human leading-strand DNA polymerase Pol ε.
Roske JJ, Yeeles JTP
Nat Struct Mol Biol (2024)
PMID: 39112807
Related structures: EMD-50222

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-248023 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA polymerase epsilon catalytic subunit A Chain: A
Molecule details ›
Chain: A
Length: 1200 amino acids
Theoretical weight: 138.14 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q07864 (Residues: 1-1200; Coverage: 53%)
Gene names: POLE, POLE1
Sequence domains:
Proliferating cell nuclear antigen Chains: B, C, D
Molecule details ›
Chains: B, C, D
Length: 261 amino acids
Theoretical weight: 28.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P12004 (Residues: 1-261; Coverage: 100%)
Gene name: PCNA
Sequence domains:
DNA nascent strand Chain: P
Molecule details ›
Chain: P
Length: 24 nucleotides
Theoretical weight: 7.07 KDa
DNA template strand Chain: T
Molecule details ›
Chain: T
Length: 38 nucleotides
Theoretical weight: 12.03 KDa

Ligands and Environments

3 bound ligands:
Ligand SF4 1 x SF4
Ligand DDS 1 x DDS
Ligand MG 1 x MG
1 modified residue:
Ligand 2DA 1 x 2DA

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-50222
Expression systems:
  • Trichoplusia ni
  • Escherichia coli BL21(DE3)

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