› 4hdv

X-ray diffraction
2.7Å resolution

Crystal structure of S. pombe ATL1 in complex with damaged DNA containing 2,6-diaminopurine

Released:
DOI: 10.2210/pdb4hdv/pdb
PDB entry 4hdv coloured by chain, front view.
PDB entry 4hdv coloured by chain, side view.
PDB entry 4hdv coloured by chain, top view.
Source organism: Schizosaccharomyces pombe
Primary publication:
Alkyltransferase-like protein (Atl1) distinguishes alkylated guanines for DNA repair using cation-π interactions.
Wilkinson OJ, Latypov V, Tubbs JL, Millington CL, Morita R, Blackburn H, Marriott A, McGown G, Thorncroft M, Watson AJ, Connolly BA, Grasby JA, Masui R, Hunter CA, Tainer JA, Margison GP, Williams DM
Proc Natl Acad Sci U S A 109 18755-60 (2012)
PMID: 23112169

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117584 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Alkyltransferase-like protein 1 Chain: A
Molecule details ›
Chain: A
Length: 116 amino acids
Theoretical weight: 13.66 KDa
Source organism: Schizosaccharomyces pombe
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UTN9 (Residues: 1-108; Coverage: 100%)
Gene names: SPAC1250.04c, atl1
Sequence domains: 6-O-methylguanine DNA methyltransferase, DNA binding domain
Structure domains: Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
5'-D(*GP*CP*CP*AP*TP*GP*(1AP)P*CP*TP*AP*GP*TP*A)-3' Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 3.99 KDa
Source organism: Schizosaccharomyces pombe
Expression system: Not provided
5'-D(*CP*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*G)-3' Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 3.95 KDa
Source organism: Schizosaccharomyces pombe
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand 1AP 1 x 1AP

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: P6122
Unit cell:
a: 59.505Å b: 59.505Å c: 237.35Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.218 0.216 0.252
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Envisioning how the prototypic molecular machine TFIIH functions in transcription initiation and DNA repair.
Tsutakawa et al. (2020)
1 more

1 mention without citation

Alkyltransferase-like protein (Atl1) distinguishes alkylated guanines for DNA repair using cation-π interactions.
Wilkinson et al. (2012)