› 2db3

X-ray diffraction
2.2Å resolution

Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa

Released:
DOI: 10.2210/pdb2db3/pdb
PDB entry 2db3 coloured by chain, front view.
PDB entry 2db3 coloured by chain, side view.
PDB entry 2db3 coloured by chain, top view.
Source organism: Drosophila melanogaster
Primary publication:
Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa.
Sengoku T, Nureki O, Nakamura A, Kobayashi S, Yokoyama S
Cell 125 287-300 (2006)
PMID: 16630817

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140543 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
ATP-dependent RNA helicase vasa Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 434 amino acids
Theoretical weight: 48.34 KDa
Source organism: Drosophila melanogaster
Expression system: Escherichia coli
UniProt:
  • Canonical: P09052 (Residues: 200-623; Coverage: 64%)
Gene names: CG46283, vas, vasa
Sequence domains:
Structure domains: P-loop containing nucleotide triphosphate hydrolases
5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3' Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 10 nucleotides
Theoretical weight: 3.02 KDa
Source organism: Drosophila melanogaster
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 4 x MG
Ligand ANP 4 x ANP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P21
Unit cell:
a: 71.05Å b: 142.331Å c: 130.465Å
α: 90° β: 90.86° γ: 90°
R-values:
R R work R free
0.197 0.197 0.25
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

83 review citations

The spliceosome: design principles of a dynamic RNP machine.
Wahl et al. (2009)
82 more

58 mentions without citation

Sequence-specific binding of single-stranded RNA: is there a code for recognition?
Auweter et al. (2006)
57 more