› 5zuo

X-ray diffraction
2.9Å resolution

Crystal Structure of BZ junction in diverse sequence

Released:
DOI: 10.2210/pdb5zuo/pdb
PDB entry 5zuo coloured by chain, front view.
PDB entry 5zuo coloured by chain, side view.
PDB entry 5zuo coloured by chain, top view.
Source organisms:
Primary publication:
Sequence preference and structural heterogeneity of BZ junctions.
Kim D, Hur J, Han JH, Ha SC, Shin D, Lee S, Park S, Sugiyama H, Kim KK
Nucleic Acids Res 46 10504-10513 (2018)
PMID: 30184200

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-119531 (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 BL21(DE3)
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*CP*GP*AP*TP*AP*AP*AP*CP*C)-3') Chain: E
Molecule details ›
Chain: E
Length: 17 nucleotides
Theoretical weight: 5.2 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*AP*CP*GP*GP*TP*TP*TP*AP*TP*CP*GP*CP*GP*CP*GP*CP*G)-3') Chain: F
Molecule details ›
Chain: F
Length: 17 nucleotides
Theoretical weight: 5.22 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 7A (6B, 6C1)
Spacegroup: P61
Unit cell:
a: 111.237Å b: 111.237Å c: 62.211Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.26 0.256 0.301
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

4 review citations

Z-DNA in the genome: from structure to disease.
Ravichandran et al. (2019)
3 more

3 mentions without citation

Recognition of non-CpG repeats in Alu and ribosomal RNAs by the Z-RNA binding domain of ADAR1 induces A-Z junctions.
Nichols et al. (2021)
2 more