PDBe 5kfr

X-ray diffraction
1.75Å resolution

Human DNA polymerase eta-DNA ternary complex with Sp-dATP-alpha-S: reaction with 20 mM Mn2+ for 600s

Released:
Source organism: Homo sapiens
Primary publication:
Capture of a third Mg²⁺ is essential for catalyzing DNA synthesis.
Science 352 1334-7 (2016)
PMID: 27284197

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase eta Chain: A
Molecule details ›
Chain: A
Length: 435 amino acids
Theoretical weight: 48.62 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9Y253 (Residues: 1-432; Coverage: 61%)
Gene names: POLH, RAD30, RAD30A, XPV
Sequence domains: impB/mucB/samB family
DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*TP*(AS))-3') Chain: P
Molecule details ›
Chain: P
Length: 9 nucleotides
Theoretical weight: 2.76 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3') Chain: T
Molecule details ›
Chain: T
Length: 12 nucleotides
Theoretical weight: 3.64 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments


1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P61
Unit cell:
a: 98.25Å b: 98.25Å c: 81.32Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.179 0.175 0.223
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided