4D25

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

RNA Clamping by Vasa Assembles a Pirna Amplifier Complex on Transposon Transcripts.

Xiol, J.Spinelli, P.Laussmann, M.A.Homolka, D.Yang, Z.Cora, E.Coute, Y.Conn, S.Kadlec, J.Sachidanandam, R.Kaksonen, M.Cusack, S.Ephrussi, A.Pillai, R.S.

(2014) Cell 157: 1698

  • DOI: 10.1016/j.cell.2014.05.018
  • Primary Citation of Related Structures:  
    4D25, 4D26

  • PubMed Abstract: 
  • Germline-specific Piwi-interacting RNAs (piRNAs) protect animal genomes against transposons and are essential for fertility. piRNAs targeting active transposons are amplified by the ping-pong cycle, which couples Piwi endonucleolytic slicing of target RNAs to biogenesis of new piRNAs ...

    Germline-specific Piwi-interacting RNAs (piRNAs) protect animal genomes against transposons and are essential for fertility. piRNAs targeting active transposons are amplified by the ping-pong cycle, which couples Piwi endonucleolytic slicing of target RNAs to biogenesis of new piRNAs. Here, we describe the identification of a transient Amplifier complex that mediates biogenesis of secondary piRNAs in insect cells. Amplifier is nucleated by the DEAD box RNA helicase Vasa and contains the two Piwi proteins participating in the ping-pong loop, the Tudor protein Qin/Kumo and antisense piRNA guides. These components assemble on the surface of Vasa's helicase domain, which functions as an RNA clamp to anchor Amplifier onto transposon transcripts. We show that ATP-dependent RNP remodeling by Vasa facilitates transfer of 5' sliced piRNA precursors between ping-pong partners, and loss of this activity causes sterility in Drosophila. Our results reveal the molecular basis for the small RNA amplification that confers adaptive immunity against transposons.


    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France. Electronic address: pillai@embl.fr.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BMVLG PROTEINA434Bombyx moriMutation(s): 2 
Gene Names: BmVLG
EC: 3.6.4.13
UniProt
Find proteins for O01378 (Bombyx mori)
Explore O01378 
Go to UniProtKB:  O01378
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-R(*UP*GP*AP*CP*AP*UP)-3'B [auth D]6Bombyx mori
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ANP
    Query on ANP

    Download Ideal Coordinates CCD File 
    C [auth A]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
    C10 H17 N6 O12 P3
    PVKSNHVPLWYQGJ-KQYNXXCUSA-N
     Ligand Interaction
    GOL
    Query on GOL

    Download Ideal Coordinates CCD File 
    E [auth D]GLYCEROL
    C3 H8 O3
    PEDCQBHIVMGVHV-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    D [auth A]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.90 Å
    • R-Value Free: 0.208 
    • R-Value Work: 0.171 
    • R-Value Observed: 0.173 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 52.48α = 90
    b = 78.57β = 90
    c = 104.58γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement
    XDSdata reduction
    XSCALEdata scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2014-06-18
      Type: Initial release
    • Version 1.1: 2014-07-02
      Changes: Database references