Crystal structure of the N-terminal domain of the Human DEAD-BOX RNA helicase DDX5 (P68)

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.262 

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The Variable N-Terminal Region of Ddx5 Contains Structural Elements and Auto-Inhibits its Interaction with Ns5B of Hepatitis C Virus.

Dutta, S.Gupta, G.Choi, Y.W.Kotaka, M.Fielding, B.C.Song, J.Tan, Y.J.

(2012) Biochem J 446: 37

  • DOI: https://doi.org/10.1042/BJ20120001
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    RNA helicases of the DEAD (Asp-Glu-Ala-Asp)-box family of proteins are involved in many aspects of RNA metabolism from transcription to RNA decay, but most of them have also been shown to be multifunctional. The DEAD-box helicase DDX5 of host cells has been shown to interact with the RNA-dependent RNA polymerase (NS5B) of HCV (hepatitis C virus). In the present study, we report the presence of two independent NS5B-binding sites in DDX5, one located at the N-terminus and another at the C-terminus. The N-terminal fragment of DDX5, which consists of the first 305 amino acids and shall be referred as DDX5-N, was expressed and crystallized. The crystal structure shows that domain 1 (residues 79-303) of DDX5 contains the typical features found in the structures of other DEAD-box helicases. DDX5-N also contains the highly variable NTR (N-terminal region) of unknown function and the crystal structure reveals structural elements in part of the NTR, namely residues 52-78. This region forms an extensive loop and an α-helix. From co-immunoprecipitation experiments, the NTR of DDX5-N was observed to auto-inhibit its interaction with NS5B. Interestingly, the α-helix in NTR is essential for this auto-inhibition and seems to mediate the interaction between the highly flexible 1-51 residues in NTR and the NS5B-binding site in DDX5-N. Furthermore, NMR investigations reveal that there is a direct interaction between DDX5 and NS5B in vitro.

  • Organizational Affiliation

    Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UniProt & NIH Common Fund Data Resources
Find proteins for P17844 (Homo sapiens)
Explore P17844 
Go to UniProtKB:  P17844
PHAROS:  P17844
GTEx:  ENSG00000108654 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17844
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.262 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.18α = 90
b = 73.801β = 90
c = 104γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-08
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Data collection, Database references, Other, Refinement description