› 3si8

X-ray diffraction
2.15Å resolution

Human DNA polymerase eta - DNA ternary complex with the 5'T of a CPD in the active site (TT2)

Released:
DOI: 10.2210/pdb3si8/pdb
PDB entry 3si8 coloured by chain, front view.
PDB entry 3si8 coloured by chain, side view.
PDB entry 3si8 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure and mechanism of human DNA polymerase eta.
Biertümpfel C, Zhao Y, Kondo Y, Ramón-Maiques S, Gregory M, Lee JY, Masutani C, Lehmann AR, Hanaoka F, Yang W
Nature 465 1044-8 (2010)
PMID: 20577208

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-116879 (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
UniProt:
  • Canonical: Q9Y253 (Residues: 1-432; Coverage: 61%)
Gene names: POLH, RAD30, RAD30A, XPV
Sequence domains:
Structure domains:
DNA (5'-D(*TP*A*AP*CP*(TTD)P*AP*TP*GP*AP*CP*GP*C)-3') Chain: T
Molecule details ›
Chain: T
Length: 12 nucleotides
Theoretical weight: 3.95 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*TP*GP*CP*GP*TP*CP*AP*TP*A)-3') Chain: P
Molecule details ›
Chain: P
Length: 9 nucleotides
Theoretical weight: 2.73 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

7 bound ligands:
Ligand DZ4 1 x DZ4
Ligand GOL 8 x GOL
Ligand 3D1 1 x 3D1
Ligand DTT 2 x DTT
Ligand EDO 5 x EDO
Ligand MG 2 x MG
Ligand CO 1 x CO
1 modified residue:
Ligand TTD 1 x TTD

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P212121
Unit cell:
a: 61.236Å b: 80.259Å c: 139.759Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.245 0.241 0.258
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

44 review citations

Y-family DNA polymerases and their role in tolerance of cellular DNA damage.
Sale et al. (2012)
43 more

5 mentions without citation

Translesion DNA synthesis and mutagenesis in eukaryotes.
Sale JE. (2013)
4 more