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 

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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 Vasa in complex with a single-stranded RNA and an ATP analog ...

    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

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent RNA helicase vasaE [auth A],
F [auth B],
G [auth C],
H [auth D]		434Drosophila melanogasterMutation(s): 0 
Gene Names: vasa, vas, CG46283
EC: 3.6.1.3 (PDB Primary Data), 3.6.4.13 (UniProt)
UniProt
Find proteins for P09052 (Drosophila melanogaster)
Explore P09052 
Go to UniProtKB:  P09052
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09052
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3'A [auth E],
B [auth F],
C [auth G],
D [auth H]		10N/A
Protein Feature View
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  • Reference Sequence
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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