4I67

Crystal structure of the RRM domain of RNA helicase HERA from T. thermophilus in complex with GGGC RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Recognition of two distinct elements in the RNA substrate by the RNA-binding domain of the T. thermophilus DEAD box helicase Hera.

Steimer, L.Wurm, J.P.Linden, M.H.Rudolph, M.G.Wohnert, J.Klostermeier, D.

(2013) Nucleic Acids Res 41: 6259-6272

  • DOI: 10.1093/nar/gkt323
  • Primary Citation of Related Structures:  
    4I67, 4I68, 4I69

  • PubMed Abstract: 
  • DEAD box helicases catalyze the ATP-dependent destabilization of RNA duplexes. Whereas duplex separation is mediated by the helicase core shared by all members of the family, flanking domains often contribute to binding of the RNA substrate. The Thermus thermophilus DEAD-box helicase Hera (for "heat-resistant RNA-binding ATPase") contains a C-terminal RNA-binding domain (RBD) ...

    DEAD box helicases catalyze the ATP-dependent destabilization of RNA duplexes. Whereas duplex separation is mediated by the helicase core shared by all members of the family, flanking domains often contribute to binding of the RNA substrate. The Thermus thermophilus DEAD-box helicase Hera (for "heat-resistant RNA-binding ATPase") contains a C-terminal RNA-binding domain (RBD). We have analyzed RNA binding to the Hera RBD by a combination of mutational analyses, nuclear magnetic resonance and X-ray crystallography, and identify residues on helix α1 and the C-terminus as the main determinants for high-affinity RNA binding. A crystal structure of the RBD in complex with a single-stranded RNA resolves the RNA-protein interactions in the RBD core region around helix α1. Differences in RNA binding to the Hera RBD and to the structurally similar RBD of the Bacillus subtilis DEAD box helicase YxiN illustrate the versatility of RNA recognition motifs as RNA-binding platforms. Comparison of chemical shift perturbation patterns elicited by different RNAs, and the effect of sequence changes in the RNA on binding and unwinding show that the RBD binds a single-stranded RNA region at the core and simultaneously contacts double-stranded RNA through its C-terminal tail. The helicase core then unwinds an adjacent RNA duplex. Overall, the mode of RNA binding by Hera is consistent with a possible function as a general RNA chaperone.


    Organizational Affiliation

    Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, D-48149 Muenster, Germany.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Heat resistant RNA dependent ATPaseA87Thermus thermophilusMutation(s): 0 
Gene Names: TT_C1895
EC: 3.6.4.13
UniProt
Find proteins for Q72GF3 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72GF3 
Go to UniProtKB:  Q72GF3
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-R(P*GP*GP*GP*(RPC))-3'B4N/A
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.33 Å
    • R-Value Free: 0.234 
    • R-Value Work: 0.177 
    • R-Value Observed: 0.179 
    • Space Group: P 61
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 88.435α = 90
    b = 88.435β = 90
    c = 28.943γ = 120
    Software Package:
    Software NamePurpose
    PHASERphasing
    PHENIXrefinement
    XDSdata reduction
    SADABSdata scaling

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2013-04-24
      Type: Initial release
    • Version 1.1: 2013-05-15
      Changes: Database references
    • Version 1.2: 2013-07-17
      Changes: Database references
    • Version 1.3: 2014-11-26
      Changes: Structure summary
    • Version 1.4: 2017-11-15
      Changes: Refinement description