2DB3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.197 
  • R-Value Observed: 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
  • Primary Citation of Related Structures:  
    2DB3

  • 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 D Biol Crystallogr 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:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent RNA helicase vasaA, B, C, D434Drosophila melanogasterMutation(s): 0 
Gene Names: vasavasCG46283
EC: 3.6.1.3 (PDB Primary Data), 3.6.4.13 (UniProt)
Find proteins for P09052 (Drosophila melanogaster)
Explore P09052 
Go to UniProtKB:  P09052
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    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 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 CCD File 
    A, B, C, D
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.20 Å
    • R-Value Free: 0.250 
    • R-Value Work: 0.197 
    • R-Value Observed: 0.197 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 71.05α = 90
    b = 142.331β = 90.86
    c = 130.465γ = 90
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    SHARPphasing
    CNSrefinement

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

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