Investigation of RNA structure in satellite panicum mosaic virus - glutaraldehyde treated

Experimental Data Snapshot

  • Resolution: 3.30 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 

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Investigation of RNA structure in satellite panicum mosaic virus.

Makino, D.L.Day, J.Larson, S.B.McPherson, A.

(2006) Virology 351: 420-431

  • DOI: https://doi.org/10.1016/j.virol.2006.03.028
  • Primary Citation of Related Structures:  
    5CVZ, 5CW0

  • PubMed Abstract: 

    Three new crystal forms of satellite panicum mosaic virus (SPMV) were grown and their structures solved from X-ray diffraction data using molecular replacement techniques. The crystals were grown under conditions of pH and ionic strength that were appreciably different then those used for the original structure determination. In rhombohedral crystals grown at pH 8.5 and low ionic strength PEG 3350 solutions, Fourier syntheses revealed segments, ten amino acid residues long, of amino-terminal polypeptides not previously seen, as well as masses of electron density within concavities on the interior of the capsid, which appeared in the neighborhoods of icosahedral five- and threefold axes. The densities were compatible with secondary structural domains of RNA, and they included a segment of double helical RNA of about four to five base pairs oriented, at least approximately, along the fivefold axes. The distribution of RNA observed for SPMV appears to be distinctly different than the encapsidated nucleic acid conformation previously suggested for another satellite virus, satellite tobacco mosaic virus. This study further shows that analysis of viruses in crystals grown under different chemical conditions may reveal additional information regarding the structure of encapsidated RNA.

  • Organizational Affiliation

    Department of Molecular Biology and Biochemistry, University of California-Irvine, 560 Steinhaus Hall, Irvine, CA 92697, USA. dmakino@berkeley.edu

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coat protein141Panicum mosaic satellite virusMutation(s): 0 
Find proteins for Q86993 (Satellite panicum mosaic virus)
Explore Q86993 
Go to UniProtKB:  Q86993
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86993
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.30 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 226.35α = 90
b = 226.35β = 90
c = 226.35γ = 90
Software Package:
Software NamePurpose
HKL-2000data processing
Omodel building

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM58868-02
CNPq - Conselho Nacional de Desenvolvimento Cientifico e TecnologicoBrazil--

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Author supporting evidence
  • Version 1.2: 2018-03-21
    Changes: Data collection
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description