1RPU

Crystal Structure of CIRV p19 bound to siRNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Size selective recognition of siRNA by an RNA silencing suppressor

Vargason, J.M.Szittya, G.Burgyan, J.Hall, T.M.T.

(2003) Cell 115: 799-811


  • PubMed Abstract: 
  • RNA silencing in plants likely exists as a defense mechanism against molecular parasites such as RNA viruses, retrotransposons, and transgenes. As a result, many plant viruses have adapted mechanisms to evade and suppress gene silencing. Tombusviruse ...

    RNA silencing in plants likely exists as a defense mechanism against molecular parasites such as RNA viruses, retrotransposons, and transgenes. As a result, many plant viruses have adapted mechanisms to evade and suppress gene silencing. Tombusviruses express a 19 kDa protein (p19), which has been shown to suppress RNA silencing in vivo and bind silencing-generated and synthetic small interfering RNAs (siRNAs) in vitro. Here we report the 2.5 A crystal structure of p19 from the Carnation Italian ringspot virus (CIRV) bound to a 21 nt siRNA and demonstrate in biochemical and in vivo assays that CIRV p19 protein acts as a molecular caliper to specifically select siRNAs based on the length of the duplex region of the RNA.


    Organizational Affiliation

    Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
19 kDa protein
A, B
172Carnation Italian ringspot virusN/A
Find proteins for Q66104 (Carnation Italian ringspot virus)
Go to UniProtKB:  Q66104
Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(P*CP*GP*UP*AP*CP*GP*CP*GP*UP*CP*AP*CP*GP*CP*GP*UP*AP*CP*GP*UP*U)-3'C,D21N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.224 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 115.400α = 90.00
b = 115.400β = 90.00
c = 128.200γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
MAR345data collection
SHARPphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-01-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description