2DB3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

Sengoku, T.Nureki, O.Nakamura, A.Kobayashi, S.Yokoyama, S.

(2006) Cell 125: 287-300

  • DOI: 10.1016/j.cell.2006.01.054

  • PubMed Abstract: 
  • DEAD-box RNA helicases, which regulate various processes involving RNA, have two RecA-like domains as a catalytic core to alter higher-order RNA structures. We determined the 2.2 A resolution structure of the core of the Drosophila DEAD-box protein V ...

    DEAD-box RNA helicases, which regulate various processes involving RNA, have two RecA-like domains as a catalytic core to alter higher-order RNA structures. We determined the 2.2 A resolution structure of the core of the Drosophila DEAD-box protein Vasa in complex with a single-stranded RNA and an ATP analog. The ATP analog intensively interacts with both of the domains, thereby bringing them into the closed form, with many interdomain interactions of conserved residues. The bound RNA is sharply bent, avoiding a clash with a conserved alpha helix in the N-terminal domain. This "wedge" helix should disrupt base pairs by bending one of the strands when a duplex is bound. Mutational analyses indicated that the interdomain interactions couple ATP hydrolysis to RNA unwinding, probably through fine positioning of the duplex relative to the wedge helix. This mechanism, which differs from those for canonical translocating helicases, may enable the targeted modulation of intricate RNA structures.


    Related Citations: 
    • Crystallization and preliminary X-ray analysis of the helicase domains of Vasa complexed with RNA and an ATP analogue
      Sengoku, T.,Nureki, O.,Dohmae, N.,Nakamura, A.,Yokoyama, S.
      (2004) ACTA CRYSTALLOGR.,SECT.D 60: 320


    Organizational Affiliation

    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent RNA helicase vasa
A, B, C, D
434Drosophila melanogasterMutation(s): 0 
Gene Names: vas (vasa)
EC: 3.6.4.13
Find proteins for P09052 (Drosophila melanogaster)
Go to UniProtKB:  P09052
Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3'E,F,G,H10N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 71.050α = 90.00
b = 142.331β = 90.86
c = 130.465γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance