› 3cvv

X-ray diffraction
2.1Å resolution

Drosophila melanogaster (6-4) photolyase bound to ds DNA with a T-T (6-4) photolesion and F0 cofactor

Released:
DOI: 10.2210/pdb3cvv/pdb
PDB entry 3cvv coloured by chain, front view.
PDB entry 3cvv coloured by chain, side view.
PDB entry 3cvv coloured by chain, top view.
Source organism: Drosophila melanogaster
Primary publication:
The archaeal cofactor F0 is a light-harvesting antenna chromophore in eukaryotes.
Glas AF, Maul MJ, Cryle M, Barends TR, Schneider S, Kaya E, Schlichting I, Carell T
Proc Natl Acad Sci U S A 106 11540-5 (2009)
PMID: 19570997

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-116156 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Photolyase/cryptochrome alpha/beta domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 543 amino acids
Theoretical weight: 62.91 KDa
Source organism: Drosophila melanogaster
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8SXK5 (Residues: 1-520; Coverage: 96%)
Gene names: CG2488, phr6-4
Sequence domains:
Structure domains:
DNA (5'-D(*DAP*DCP*DAP*DGP*DCP*DGP*DGP*(64T)P*(5PY)P*DGP*DCP*DAP*DGP*DGP*DT)-3') Chain: C
Molecule details ›
Chain: C
Length: 15 nucleotides
Theoretical weight: 4.65 KDa
Source organism: Drosophila melanogaster
Expression system: Not provided
DNA (5'-D(*DTP*DAP*DCP*DCP*DTP*DGP*DCP*DAP*DAP*DCP*DCP*DGP*DCP*DTP*DG)-3') Chain: D
Molecule details ›
Chain: D
Length: 15 nucleotides
Theoretical weight: 4.53 KDa
Source organism: Drosophila melanogaster
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand EDO 4 x EDO
Ligand FAD 1 x FAD
Ligand FO1 1 x FO1
2 modified residues:
Ligand 64T 1 x 64T
Ligand 5PY 1 x 5PY

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P212121
Unit cell:
a: 84.59Å b: 91.07Å c: 88.26Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.168 0.166 0.213
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

8 review citations

The cryptochromes: blue light photoreceptors in plants and animals.
Chaves et al. (2011)
7 more

5 mentions without citation

Crystal structure of a prokaryotic (6-4) photolyase with an Fe-S cluster and a 6,7-dimethyl-8-ribityllumazine antenna chromophore.
Zhang et al. (2013)
4 more