› 1s0o

X-ray diffraction
2.1Å resolution

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

Released:
DOI: 10.2210/pdb1s0o/pdb
PDB entry 1s0o coloured by chain, front view.
PDB entry 1s0o coloured by chain, side view.
PDB entry 1s0o 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-114560 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chains: A, B
Molecule details ›
Chains: A, B
Length: 352 amino acids
Theoretical weight: 40.26 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q97W02 (Residues: 1-352; Coverage: 100%)
Gene names: SSO2448, dbh, dpo4
Sequence domains:
Structure domains:
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*C)-3' Chains: C, E
Molecule details ›
Chains: C, E
Length: 13 nucleotides
Theoretical weight: 4.08 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided
5'-D(*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' Chains: D, F
Molecule details ›
Chains: D, F
Length: 17 nucleotides
Theoretical weight: 5.07 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand CA 6 x CA
Ligand MG 2 x MG
Ligand TTP 2 x TTP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P212121
Unit cell:
a: 98.301Å b: 103.046Å c: 105.912Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.229 0.229 0.269
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

19 review citations

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

5 mentions without citation

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