› 4d26

X-ray diffraction
2.1Å resolution

Crystal structure of the Bombyx mori Vasa helicase (E339Q) in complex with RNA,ADP and Pi

Released:
DOI: 10.2210/pdb4d26/pdb
PDB entry 4d26 coloured by chain, front view.
PDB entry 4d26 coloured by chain, side view.
PDB entry 4d26 coloured by chain, top view.
Source organism: Bombyx mori
Primary publication:
RNA clamping by Vasa assembles a piRNA amplifier complex on transposon transcripts.
Xiol J, Spinelli P, Laussmann MA, Homolka D, Yang Z, Cora E, Couté Y, Conn S, Kadlec J, Sachidanandam R, Kaksonen M, Cusack S, Ephrussi A, Pillai RS
Cell 157 1698-711 (2014)
PMID: 24910301

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-126403 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
RNA helicase Chain: A
Molecule details ›
Chain: A
Length: 434 amino acids
Theoretical weight: 48.13 KDa
Source organism: Bombyx mori
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O01378 (Residues: 135-564; Coverage: 72%)
Gene names: 692765, BmVLG
Sequence domains:
Structure domains: P-loop containing nucleotide triphosphate hydrolases
5'-R(*UP*GP*AP*CP*AP*UP)-3' Chain: D
Molecule details ›
Chain: D
Length: 6 nucleotides
Theoretical weight: 1.88 KDa
Source organism: Bombyx mori
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand ADP 1 x ADP
Ligand PO4 1 x PO4
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: P212121
Unit cell:
a: 52.96Å b: 77.81Å c: 107.3Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.229 0.225 0.277
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

38 review citations

PIWI-interacting RNAs: small RNAs with big functions.
Ozata et al. (2019)
37 more

2 mentions without citation

Global DNA methylation profiling reveals silencing of a secreted form of Epha7 in mouse and human germinal center B-cell lymphomas.
Dawson et al. (2007)
1 more