› 1jx4

X-ray diffraction
1.7Å resolution

Crystal Structure of a Y-family DNA Polymerase in a Ternary Complex with DNA Substrates and an Incoming Nucleotide

Released:
DOI: 10.2210/pdb1jx4/pdb
PDB entry 1jx4 coloured by chain, front view.
PDB entry 1jx4 coloured by chain, side view.
PDB entry 1jx4 coloured by chain, top view.
Source organism: Saccharolobus solfataricus
Primary publication:
Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication.
Ling H, Boudsocq F, Woodgate R, Yang W
Cell 107 91-102 (2001)
PMID: 11595188

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-114037 (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: 40.54 KDa
Source organism: Saccharolobus solfataricus
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*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3' Chain: P
Molecule details ›
Chain: P
Length: 13 nucleotides
Theoretical weight: 4.11 KDa
Source organism: Saccharolobus solfataricus
Expression system: Not provided
5'-D(*T*TP*CP*AP*TP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' Chain: T
Molecule details ›
Chain: T
Length: 18 nucleotides
Theoretical weight: 5.35 KDa
Source organism: Saccharolobus solfataricus
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand CA 1 x CA
Ligand MG 1 x MG
Ligand ADI 1 x ADI
1 modified residue:
Ligand MSE 6 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X9B
Spacegroup: P21212
Unit cell:
a: 97.09Å b: 102.82Å c: 52.3Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.213 0.213 0.228
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

69 review citations

Eukaryotic translesion synthesis DNA polymerases: specificity of structure and function.
Prakash et al. (2005)
68 more

38 mentions without citation

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