› 7m8d

X-ray diffraction
1.92Å resolution

Human DNA Pol eta S113A with rA-ended primer and dATP: in crystallo reaction for 300 s

Released:
DOI: 10.2210/pdb7m8d/pdb
PDB entry 7m8d coloured by chain, front view.
PDB entry 7m8d coloured by chain, side view.
PDB entry 7m8d coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction.
Gregory MT, Gao Y, Cui Q, Yang W
Proc Natl Acad Sci U S A 118 (2021)
PMID: 34088846

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-113266 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
1 distinct DNA/RNA hybrid molecule
Macromolecules (3 distinct):
DNA polymerase eta Chain: A
Molecule details ›
Chain: A
Length: 435 amino acids
Theoretical weight: 48.6 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y253 (Residues: 1-432; Coverage: 61%)
Gene names: POLH, RAD30, RAD30A, XPV
Sequence domains:
DNA (5'-D(*CP*AP*TP*TP*TP*TP*GP*AP*CP*GP*CP*T)-3') Chain: T
Molecule details ›
Chain: T
Length: 12 nucleotides
Theoretical weight: 3.63 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA/RNA (5'-D(*AP*GP*CP*GP*TP*CP*A)-R(P*A)-D(P*A)-3') Chain: P
Molecule details ›
Chain: P
Length: 9 nucleotides
Theoretical weight: 2.76 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand MG 3 x MG
Ligand GOL 2 x GOL
Ligand DTP 1 x DTP
Ligand DPO 1 x DPO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P61
Unit cell:
a: 98.422Å b: 98.422Å c: 81.618Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.167 0.162 0.217
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 citation in other articles

In crystallo observation of three metal ion promoted DNA polymerase misincorporation.
Chang et al. (2022)
4 more