1DI2

CRYSTAL STRUCTURE OF A DSRNA-BINDING DOMAIN COMPLEXED WITH DSRNA: MOLECULAR BASIS OF DOUBLE-STRANDED RNA-PROTEIN INTERACTIONS

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Molecular basis of double-stranded RNA-protein interactions: structure of a dsRNA-binding domain complexed with dsRNA.

Ryter, J.M., Schultz, S.C.

(1998) EMBO J 17: 7505-7513

  • DOI: 10.1093/emboj/17.24.7505
  • Primary Citation of Related Structures:  
    1DI2

  • PubMed Abstract: 

    • Protein interactions with double-stranded RNA (dsRNA) are critical for many cell processes; however, in contrast to protein-dsDNA interactions, surprisingly little is known about the molecular basis of protein-dsRNA interactions. A large and diverse class of proteins that bind dsRNA do so by utilizing an approximately 70 amino acid motif referred to as the dsRNA-binding domain (dsRBD) ...

    Protein interactions with double-stranded RNA (dsRNA) are critical for many cell processes; however, in contrast to protein-dsDNA interactions, surprisingly little is known about the molecular basis of protein-dsRNA interactions. A large and diverse class of proteins that bind dsRNA do so by utilizing an approximately 70 amino acid motif referred to as the dsRNA-binding domain (dsRBD). We have determined a 1.9 A resolution crystal structure of the second dsRBD of Xenopus laevis RNA-binding protein A complexed with dsRNA. The structure shows that the protein spans 16 bp of dsRNA, interacting with two successive minor grooves and across the intervening major groove on one face of a primarily A-form RNA helix. The nature of these interactions explains dsRBD specificity for dsRNA (over ssRNA or dsDNA) and the apparent lack of sequence specificity. Interestingly, the dsRBD fold resembles a portion of the conserved core structure of a family of polynucleotidyl transferases that includes RuvC, MuA transposase, retroviral integrase and RNase H. Structural comparisons of the dsRBD-dsRNA complex and models proposed for polynucleotidyl transferase-nucleic acid complexes suggest that similarities in nucleic acid binding also exist between these families of proteins.

    Organizational Affiliation: 

    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA.



Macromolecules

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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DOUBLE STRANDED RNA BINDING PROTEIN AE [auth A], F [auth B]69Xenopus laevisMutation(s): 1 
Gene Names: prkra-b, rbpa
UniProt
Find proteins for Q91836 (Xenopus laevis)
Explore Q91836 
Go to UniProtKB:  Q91836
Protein Feature View
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  • Reference Sequence
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    • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')A [auth C], B [auth D], C [auth E], D [auth G]10N/A
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.90 Å
    • R-Value Free: 0.258 
    • R-Value Work: 0.228 
    • R-Value Observed: 0.231 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 110.4α = 90
    b = 58.5β = 105.2
    c = 58.9γ = 90
    Software Package:
    Software NamePurpose
    MLPHAREphasing
    CNSrefinement
    DENZOdata reduction
    SCALEPACKdata scaling

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1999-12-02
      Type: Initial release
    • Version 1.1: 2008-04-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance