3VYY

Structural insights into RISC assembly facilitated by dsRNA binding domains of human RNA helicase A (DHX9)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into RISC assembly facilitated by dsRNA-binding domains of human RNA helicase A (DHX9)

Fu, Q.Yuan, Y.A.

(2013) Nucleic Acids Res 

  • DOI: 10.1093/nar/gkt042
  • Primary Citation of Related Structures:  
    3VYX, 3VYY

  • PubMed Abstract: 
  • Intensive research interest has focused on small RNA-processing machinery and the RNA-induced silencing complex (RISC), key cellular machines in RNAi pathways. However, the structural mechanism regarding RISC assembly, the primary step linking small RNA ...

    Intensive research interest has focused on small RNA-processing machinery and the RNA-induced silencing complex (RISC), key cellular machines in RNAi pathways. However, the structural mechanism regarding RISC assembly, the primary step linking small RNA processing and RNA-mediated gene silencing, is largely unknown. Human RNA helicase A (DHX9) was reported to function as an RISC-loading factor, and such function is mediated mainly by its dsRNA-binding domains (dsRBDs). Here, we report the crystal structures of human RNA helicase A (RHA) dsRBD1 and dsRBD2 domains in complex with dsRNAs, respectively. Structural analysis not only reveals higher siRNA duplex-binding affinity displayed by dsRBD1, but also identifies a crystallographic dsRBD1 pair of physiological significance in cooperatively recognizing dsRNAs. Structural observations are further validated by isothermal titration calorimetric (ITC) assay. Moreover, co-immunoprecipitation (co-IP) assay coupled with mutagenesis demonstrated that both dsRBDs are required for RISC association, and such association is mediated by dsRNA. Hence, our structural and functional efforts have revealed a potential working model for siRNA recognition by RHA tandem dsRBDs, and together they provide direct structural insights into RISC assembly facilitated by RHA.


    Organizational Affiliation

    Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent RNA helicase A AB91Homo sapiensMutation(s): 0 
Gene Names: DHX9DDX9LKPNDH2
EC: 3.6.4.13
Find proteins for Q08211 (Homo sapiens)
Explore Q08211 
Go to UniProtKB:  Q08211
NIH Common Fund Data Resources
PHAROS:  Q08211
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3')C, D, E, F, G10synthetic construct
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.90 Å
    • R-Value Free: 0.262 
    • R-Value Work: 0.219 
    • R-Value Observed: 0.221 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 52.252α = 90
    b = 78.529β = 98.81
    c = 112.242γ = 90
    Software Package:
    Software NamePurpose
    HKL-2000data collection
    MOLREPphasing
    REFMACrefinement
    HKL-2000data reduction
    HKL-2000data scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    • Deposited Date: 2012-10-05 
    • Released Date: 2013-02-13 
    • Deposition Author(s): Yuan, Y.A., Fu, Q.

    Revision History 

    • Version 1.0: 2013-02-13
      Type: Initial release
    • Version 1.1: 2019-12-04
      Changes: Data collection, Source and taxonomy