› 3bjy

X-ray diffraction
2.41Å resolution

Catalytic core of Rev1 in complex with DNA (modified template guanine) and incoming nucleotide

Released:
DOI: 10.2210/pdb3bjy/pdb
PDB entry 3bjy coloured by chain, front view.
PDB entry 3bjy coloured by chain, side view.
PDB entry 3bjy coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Protein-template-directed synthesis across an acrolein-derived DNA adduct by yeast Rev1 DNA polymerase.
Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK
Structure 16 239-45 (2008)
PMID: 18275815

Function and Biology Details

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-116094 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA repair protein REV1 Chain: A
Molecule details ›
Chain: A
Length: 434 amino acids
Theoretical weight: 49.45 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P12689 (Residues: 305-738; Coverage: 44%)
Gene names: O6339, REV1, YOR346W
Sequence domains:
Structure domains:
DNA (5'-D(*DTP*DAP*DAP*(P)P*DGP*DTP*DAP*DGP*DGP*DGP*DGP*DAP*DGP*DGP*DAP*DT)-3') Chain: T
Molecule details ›
Chain: T
Length: 16 nucleotides
Theoretical weight: 5.11 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided
DNA (5'-D(*DAP*DTP*DCP*DCP*DTP*DCP*DCP*DCP*DCP*DTP*DAP*(DOC))-3') Chain: P
Molecule details ›
Chain: P
Length: 12 nucleotides
Theoretical weight: 3.5 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand DCP 1 x DCP
Ligand MG 2 x MG
2 modified residues:
Ligand P 1 x P
Ligand DOC 1 x DOC

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: C2221
Unit cell:
a: 181.062Å b: 199.578Å c: 55.677Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.231 0.231 0.241
Expression systems:
  • Saccharomyces cerevisiae
  • Not provided

Quick links

Citations

13 review citations

Eukaryotic translesion polymerases and their roles and regulation in DNA damage tolerance.
Waters et al. (2009)
12 more

4 mentions without citation

Variations on a theme: eukaryotic Y-family DNA polymerases.
Washington et al. (2010)
3 more