6BJV

CIRV p19 protein in complex with siRNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.262 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural insights into interactions between viral suppressor of RNA silencing protein p19 mutants and small RNAs.

Foss, D.V., Schirle, N.T., MacRae, I.J., Pezacki, J.P.

(2019) FEBS Open Bio 9: 1042-1051

  • DOI: 10.1002/2211-5463.12644
  • Primary Citation of Related Structures:  
    6BJG, 6BJH, 6BJV

  • PubMed Abstract: 

    • Viral suppressors of RNA silencing (VSRSs) are a diverse group of viral proteins that have evolved to disrupt eukaryotic RNA silencing pathways, thereby contributing to viral pathogenicity. The p19 protein is a VSRS that selectively binds to short interfering RNAs (siRNAs) over microRNAs (miRNAs) ...

    Viral suppressors of RNA silencing (VSRSs) are a diverse group of viral proteins that have evolved to disrupt eukaryotic RNA silencing pathways, thereby contributing to viral pathogenicity. The p19 protein is a VSRS that selectively binds to short interfering RNAs (siRNAs) over microRNAs (miRNAs). Mutational analysis has identified single amino acid substitutions that reverse this selectivity through new high-affinity interactions with human miR-122. Herein, we report crystal structures of complexed p19-T111S (2.6 Å), p19-T111H (2.3 Å) and wild-type p19 protein (2.2 Å) from the Carnation Italian ringspot virus with small interfering RNA (siRNA) ligands. Structural comparisons reveal that these mutations do not lead to major changes in p19 architecture, but instead promote subtle rearrangement of residues and solvent molecules along the p19 midline. These observations suggest p19 uses many small interactions to distinguish siRNAs from miRNAs and perturbing these interactions can create p19 variants with novel RNA-recognition properties. DATABASE: Model data are deposited in the PDB database under the accession numbers 6BJG, 6BJH and 6BJV.

    Related Citations: 
    • Enhanced specificity of the viral suppressor of RNA silencing protein p19 toward sequestering of human microRNA-122
      Cheng, J., Danielson, D.C., Nasheri, N., Singaravelu, R., Pezacki, J.P.
      (2011) Biochemistry 50: 7745
    Organizational Affiliation: 

    Department of Chemistry and Biomolecular Sciences, University of Ottawa, Canada.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA silencing suppressor p19A, B172Carnation Italian ringspot virusMutation(s): 0 
Gene Names: ORF4
UniProt
Find proteins for Q66104 (Carnation Italian ringspot virus)
Explore Q66104 
Go to UniProtKB:  Q66104
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ66104
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*UP*CP*GP*AP*AP*GP*UP*AP*UP*UP*CP*CP*GP*CP*GP*UP*AP*CP*GP*UP*U)-3')C 21Lampyridae
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP*AP*UP*U)-3')D 21Lampyridae
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.262 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.586α = 109.44
b = 46.997β = 111.11
c = 54.883γ = 96.78
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-07-03
    Changes: Data collection, Database references