5N96

Crystal Structure of Drosophila DHX36 helicase in complex with AGGGTTTTTT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular Mechanistic Insights into Drosophila DHX36-Mediated G-Quadruplex Unfolding: A Structure-Based Model.

Chen, W.F.Rety, S.Guo, H.L.Dai, Y.X.Wu, W.Q.Liu, N.N.Auguin, D.Liu, Q.W.Hou, X.M.Dou, S.X.Xi, X.G.

(2018) Structure 26: 403-415.e4

  • DOI: 10.1016/j.str.2018.01.008
  • Primary Citation of Related Structures:  
    5N98, 5N90, 5N8R, 5N8S, 5N94, 5N96, 5N9A, 5N9D

  • PubMed Abstract: 
  • Helicase DHX36 plays essential roles in cell development and differentiation at least partially by resolving G-quadruplex (G4) structures. Here we report crystal structures of the Drosophila homolog of DHX36 (DmDHX36) in complex with RNA and a series of ...

    Helicase DHX36 plays essential roles in cell development and differentiation at least partially by resolving G-quadruplex (G4) structures. Here we report crystal structures of the Drosophila homolog of DHX36 (DmDHX36) in complex with RNA and a series of DNAs. By combining structural, small-angle X-ray scattering, molecular dynamics simulation, and single-molecule fluorescence studies, we revealed that positively charged amino acids in RecA2 and OB-like domains constitute an elaborate structural pocket at the nucleic acid entrance, in which negatively charged G4 DNA is tightly bound and partially destabilized. The G4 DNA is then completely unfolded through the 3'-5' translocation activity of the helicase. Furthermore, crystal structures and DNA binding assays show that G-rich DNA is preferentially recognized and in the presence of ATP, specifically bound by DmDHX36, which may cooperatively enhance the G-rich DNA translocation and G4 unfolding. On the basis of these results, a conceptual G4 DNA-resolving mechanism is proposed.


    Organizational Affiliation

    College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; LBPA, ENS de Cachan, Université Paris-Saclay, Centre National de la Recherche Scientifique, 61 Avenue du Président Wilson, 94235 Cachan, France. Electronic address: xxi01@ens-cachan.fr.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CG9323, isoform A AB944Drosophila melanogasterMutation(s): 0 
Gene Names: CG9323Dmel_CG9323Rhau38E.15cg9323DmDHX36Dmel\CG9323DmRHAURHAU
EC: 3.6.1.3 (PDB Primary Data), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt)
Find proteins for Q8SWT2 (Drosophila melanogaster)
Explore Q8SWT2 
Go to UniProtKB:  Q8SWT2
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*AP*GP*GP*GP*TP*TP*TP*TP*TP*T)-3')C, D10Homo sapiens
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    A, B
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.72 Å
    • R-Value Free: 0.248 
    • R-Value Work: 0.180 
    • R-Value Observed: 0.183 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 303.389α = 90
    b = 51.316β = 114.57
    c = 164.602γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    XDSdata reduction
    Aimlessdata scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2018-03-14
      Type: Initial release
    • Version 1.1: 2019-02-20
      Changes: Advisory, Data collection, Derived calculations