› 5wmb

X-ray diffraction
2.25Å resolution

Structure of the 10S (-)-cis-BP-dG modified Rev1 ternary complex (the BP residue is disordered)

Released:
DOI: 10.2210/pdb5wmb/pdb
PDB entry 5wmb coloured by chain, front view.
PDB entry 5wmb coloured by chain, side view.
PDB entry 5wmb coloured by chain, top view.
Source organisms:
Primary publication:
Mechanism of error-free replication across benzo[a]pyrene stereoisomers by Rev1 DNA polymerase.
Rechkoblit O, Kolbanovskiy A, Landes H, Geacintov NE, Aggarwal AK
Nat Commun 8 965 (2017)
PMID: 29042535

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-119347 (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 S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P12689 (Residues: 305-738; Coverage: 44%)
Gene names: O6339, REV1, YOR346W
Sequence domains:
Structure domains:
DNA (5'-D(*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*(DDG))-3') Chain: P
Molecule details ›
Chain: P
Length: 12 nucleotides
Theoretical weight: 3.8 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*AP*TP*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*C)-3') Chain: T
Molecule details ›
Chain: T
Length: 17 nucleotides
Theoretical weight: 5.04 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand MG 4 x MG
Ligand DCP 1 x DCP
Ligand GOL 4 x GOL
Ligand EDO 7 x EDO
Ligand PEG 1 x PEG
1 modified residue:
Ligand DDG 1 x DDG

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P212121
Unit cell:
a: 63.307Å b: 65.476Å c: 131.657Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.172 0.17 0.217
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Structure and function relationships in mammalian DNA polymerases.
Hoitsma et al. (2020)
1 more

1 mention without citation

Mechanism of error-free replication across benzo[a]pyrene stereoisomers by Rev1 DNA polymerase.
Rechkoblit et al. (2017)