Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 52078.74 
• Atom Count: 3944 
• Residue Count: 386 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

1RPU

Crystal Structure of CIRV p19 bound to siRNA

• DOI: 10.2210/pdb1RPU/pdb
• NDB: PR0109

• Classification: RNA Binding Protein/RNA
• Organism(s): Carnation Italian ringspot virus
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2003-12-03 Released: 2004-01-13 
• Deposition Author(s): Vargason, J.M., Szittya, G., Burgyan, J., Hall, T.M.T.

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Experimental Data Snapshot

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

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: 14697199 


• 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. 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
19 kDa protein	A, B	172	Carnation Italian ringspot virus	Mutation(s): 0
Find proteins for Q66104 (Carnation Italian ringspot virus) Go to UniProtKB:  Q66104

Entity ID: 1
Molecule	Chains	Length	Organism
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,D	21	N/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 = 115.400	α = 90.00
b = 115.400	β = 90.00
c = 128.200	γ = 120.00

Software Package:

Software Name	Purpose
CNS	refinement
MAR345	data collection
SHARP	phasing
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-12-03 
• Released Date: 2004-01-13 
• Deposition Author(s): Vargason, J.M., Szittya, G., Burgyan, J., Hall, T.M.T.

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