› 3irq

X-ray diffraction
2.8Å resolution

Crystal structure of a Z-Z junction

Released:
DOI: 10.2210/pdb3irq/pdb
PDB entry 3irq coloured by chain, front view.
PDB entry 3irq coloured by chain, side view.
PDB entry 3irq coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of a junction between two Z-DNA helices.
de Rosa M, de Sanctis D, Rosario AL, Archer M, Rich A, Athanasiadis A, Carrondo MA
Proc Natl Acad Sci U S A 107 9088-92 (2010)
PMID: 20439751

Function and Biology Details

Reaction catalysed: 
Adenine in double-stranded RNA + H(2)O = hypoxanthine in double-stranded RNA + NH(3)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116416 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Double-stranded RNA-specific adenosine deaminase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 67 amino acids
Theoretical weight: 7.37 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P55265 (Residues: 140-202; Coverage: 5%)
Gene names: ADAR, ADAR1, DSRAD, G1P1, IFI4
Sequence domains: Adenosine deaminase z-alpha domain
Structure domains: Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
DNA (5'-D(*GP*TP*CP*GP*CP*GP*CP*GP*TP*CP*GP*CP*GP*CP*G)-3') Chain: G
Molecule details ›
Chain: G
Length: 15 nucleotides
Theoretical weight: 4.6 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*AP*CP*CP*GP*CP*GP*CP*GP*AP*CP*GP*CP*GP*CP*G)-3') Chain: F
Molecule details ›
Chain: F
Length: 15 nucleotides
Theoretical weight: 4.58 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P212121
Unit cell:
a: 29.283Å b: 99.761Å c: 106.482Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.236 0.235 0.271
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

Cytidine deaminases: AIDing DNA demethylation?
Fritz et al. (2010)
6 more

6 mentions without citation

Making the bend: DNA tertiary structure and protein-DNA interactions.
Harteis et al. (2014)
5 more