› 7u78

X-ray diffraction
1.61Å resolution

Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 1.0 mM Mg2+ for 80s

Released:
DOI: 10.2210/pdb7u78/pdb
PDB entry 7u78 coloured by chain, front view.
PDB entry 7u78 coloured by chain, side view.
PDB entry 7u78 coloured by chain, top view.
Source organisms:
Primary publication:
In crystallo observation of three metal ion promoted DNA polymerase misincorporation.
Chang C, Lee Luo C, Gao Y
OpenAccess logo Nat Commun 13 2346 (2022)
PMID: 35487947

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-122152 (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:
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: synthetic construct
Expression system: Not provided
DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*TP*G)-3') Chain: P
Molecule details ›
Chain: P
Length: 8 nucleotides
Theoretical weight: 2.43 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand MG 3 x MG
Ligand CA 1 x CA
Ligand GOL 2 x GOL
Ligand DGT 1 x DGT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P61
Unit cell:
a: 97.742Å b: 97.742Å c: 81.762Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.188 0.186 0.217
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

New insights into DNA polymerase mechanisms provided by time-lapse crystallography.
Weaver et al. (2022)
1 more