› 1s0n

X-ray diffraction
2.8Å resolution

Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift

Released:
DOI: 10.2210/pdb1s0n/pdb
PDB entry 1s0n coloured by chain, front view.
PDB entry 1s0n coloured by chain, side view.
PDB entry 1s0n coloured by chain, top view.
Source organism: Saccharolobus solfataricus P2
Primary publication:
Snapshots of replication through an abasic lesion; structural basis for base substitutions and frameshifts.
Ling H, Boudsocq F, Woodgate R, Yang W
Mol Cell 13 751-62 (2004)
PMID: 15023344

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114559 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chain: A
Molecule details ›
Chain: A
Length: 352 amino acids
Theoretical weight: 40.26 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97W02 (Residues: 1-352; Coverage: 100%)
Gene names: SSO2448, dbh, dpo4
Sequence domains:
Structure domains:
5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*AP*CP*G)-3' Chain: P
Molecule details ›
Chain: P
Length: 13 nucleotides
Theoretical weight: 3.98 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided
5'-D(*TP*AP*CP*GP*AP*CP*GP*TP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3' Chain: T
Molecule details ›
Chain: T
Length: 18 nucleotides
Theoretical weight: 5.52 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand CA 3 x CA
Ligand DCP 1 x DCP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P21212
Unit cell:
a: 99.112Å b: 102.66Å c: 53.176Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.238 0.238 0.275
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

17 review citations

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

6 mentions without citation

An overview of Y-Family DNA polymerases and a case study of human DNA polymerase η.
Yang W. (2014)
5 more