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 

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:  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 Ther ...

    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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heat resistant RNA dependent ATPase
A
87Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)N/A
Find proteins for Q72GF3 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72GF3
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(P*GP*GP*GP*(RPC))-3'B4N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
RPC
Query on RPC
B
RNA LINKINGC9 H15 N3 O11 P2C
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.177 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 88.435α = 90.00
b = 88.435β = 90.00
c = 28.943γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
SADABSdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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