› 2vtb

X-ray diffraction
2.01Å resolution

Structure of cryptochrome 3 - DNA complex

Released:
DOI: 10.2210/pdb2vtb/pdb
Model geometry
Fit model/data
PDB entry 2vtb coloured by chain, front view.
PDB entry 2vtb coloured by chain, side view.
PDB entry 2vtb coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Recognition and repair of UV lesions in loop structures of duplex DNA by DASH-type cryptochrome.
Pokorny R, Klar T, Hennecke U, Carell T, Batschauer A, Essen LO
Proc Natl Acad Sci U S A 105 21023-7 (2008)
PMID: 19074258

Function and Biology Details

Reaction catalysed: 
Cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115884 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (3 distinct):
Cryptochrome DASH, chloroplastic/mitochondrial Chains: A, C, D, E, F
Molecule details ›
Chains: A, C, D, E, F
Length: 526 amino acids
Theoretical weight: 60.46 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q84KJ5 (Residues: 44-569; Coverage: 92%)
Gene names: At5g24850, CRY3, CRYD, F6A4.60
Sequence domains:
Structure domains:
Cryptochrome DASH, chloroplastic/mitochondrial Chain: B
Molecule details ›
Chain: B
Length: 525 amino acids
Theoretical weight: 60.39 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q84KJ5 (Residues: 44-569; Coverage: 92%)
Gene names: At5g24850, CRY3, CRYD, F6A4.60
Sequence domains:
Structure domains:
5'-D(*DT*DT*DT*DT*DTP)-3' Chains: G, H, I, J, K, L

Ligands and Environments


Cofactor: Ligand FAD 6 x FAD
3 bound ligands:
Ligand MHF 6 x MHF
Ligand CL 8 x CL
Ligand ACT 1 x ACT
1 modified residue:
Ligand TCP 6 x TCP

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: EMBL/DESY, HAMBURG BEAMLINE BW7A
Spacegroup: P212121
Unit cell:
a: 120.734Å b: 136.082Å c: 211.484Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.185 0.184 0.222
Expression system: Escherichia coli

Quick links

Citations

30 review citations

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

10 mentions without citation

Recognition and repair of UV lesions in loop structures of duplex DNA by DASH-type cryptochrome.
Pokorny et al. (2008)
9 more