› 1v3p

X-ray diffraction
2.3Å resolution

Crystal structure of d(GCGAGAGC): the DNA octaplex structure with I-motif of G-quartet

Released:
DOI: 10.2210/pdb1v3p/pdb
PDB entry 1v3p coloured by chain, front view.
PDB entry 1v3p coloured by chain, side view.
PDB entry 1v3p coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats.
Kondo J, Adachi W, Umeda S, Sunami T, Takénaka A
Nucleic Acids Res 32 2541-9 (2004)
PMID: 15133122

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114716 (preferred)
Entry contents:
1 distinct DNA molecule
Macromolecule:
5'-D(*GP*(C38)P*GP*AP*GP*AP*GP*C)-3' Chains: A, B
Molecule details ›
Chains: A, B
Length: 8 nucleotides
Theoretical weight: 2.6 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand K 2 x K
1 modified residue:
Ligand C38 2 x C38

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-18B
Spacegroup: I222
Unit cell:
a: 36.18Å b: 36.38Å c: 63.12Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.234 0.234 0.265
Expression system: Not provided

Quick links

Citations

3 review citations

DNA architecture: from G to Z.
Phan et al. (2006)
2 more

3 mentions without citation

DNA conformations and their sequence preferences.
Svozil et al. (2008)
2 more