› 4gem

X-ray diffraction
2.21Å resolution

Crystal structure of Zucchini (K171A)

Released:
DOI: 10.2210/pdb4gem/pdb
PDB entry 4gem coloured by chain, front view.
PDB entry 4gem coloured by chain, side view.
PDB entry 4gem coloured by chain, top view.
Source organism: Drosophila melanogaster
Primary publication:
Structure and function of Zucchini endoribonuclease in piRNA biogenesis.
Nishimasu H, Ishizu H, Saito K, Fukuhara S, Kamatani MK, Bonnefond L, Matsumoto N, Nishizawa T, Nakanaga K, Aoki J, Ishitani R, Siomi H, Siomi MC, Nureki O
Nature 491 284-7 (2012)
PMID: 23064230

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-194273 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Mitochondrial cardiolipin hydrolase Chains: A, B
Molecule details ›
Chains: A, B
Length: 220 amino acids
Theoretical weight: 24.74 KDa
Source organism: Drosophila melanogaster
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9VKD7 (Residues: 41-253; Coverage: 84%)
Gene names: CG12314, zuc
Sequence domains: PLD-like domain
Structure domains: Endonuclease Chain A

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32XU
Spacegroup: P21
Unit cell:
a: 55.883Å b: 70.214Å c: 56.938Å
α: 90° β: 108.76° γ: 90°
R-values:
R R work R free
0.193 0.19 0.246
Expression system: Escherichia coli

Quick links

Citations

84 review citations

Regulation of microRNA biogenesis.
Ha et al. (2014)
83 more

3 mentions without citation

Crystal Structure of a Phospholipase D from the Plant-Associated Bacteria Serratia plymuthica Strain AS9 Reveals a Unique Arrangement of Catalytic Pocket.
Wang et al. (2021)
2 more