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Science 17 December 2004:
Vol. 306. no. 5704, pp. 2108 - 2111
DOI: 10.1126/science.1103399
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Reports

Cofolding Organizes Alfalfa Mosaic Virus RNA and Coat Protein for Replication

Laura M. Guogas,1,3 David J. Filman,2 James M. Hogle,2* Lee Gehrke1,3*

Alfalfa mosaic virus genomic RNAs are infectious only when the viral coat protein binds to the RNA 3' termini. The crystal structure of an alfalfa mosaic virus RNA-peptide complex reveals that conserved AUGC repeats and Pro-Thr-x-Arg-Ser-x-x-Tyr coat protein amino acids cofold upon interacting. Alternating AUGC residues have opposite orientation, and they base pair in different adjacent duplexes. Localized RNA backbone reversals stabilized by arginine-guanine interactions place the adenosines and guanines in reverse order in the duplex. The results suggest that a uniform, organized 3' conformation, similar to that found on viral RNAs with transfer RNA–like ends, may be essential for replication.

1 Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA.
2 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
3 Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

* To whom correspondence should be addressed. E-mail: Lee_Gehrke{at}hms.harvard.edu (L.G.); James_Hogle{at}hms.harvard.edu (J.M.H.)

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THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
A Phylogenetic Method for Detecting Positive Epistasis in Gene Sequences and Its Application to RNA Virus Evolution.
B. Shapiro, A. Rambaut, O. G. Pybus, and E. C. Holmes (2006)
Mol. Biol. Evol. 23, 1724-1730
   Abstract »    Full Text »    PDF »
The Capsid Protein of Satellite Panicum Mosaic Virus Contributes to Systemic Invasion and Interacts with Its Helper Virus.
R. T. Omarov, D. Qi, and K.-B. G. Scholthof (2005)
J. Virol. 79, 9756-9764
   Abstract »    Full Text »    PDF »
Evaluation of the Conformational Switch Model for Alfalfa Mosaic Virus RNA Replication.
J. E. Petrillo, G. Rocheleau, B. Kelley-Clarke, and L. Gehrke (2005)
J. Virol. 79, 5743-5751
   Abstract »    Full Text »    PDF »
Coat Protein Activation of Alfalfa Mosaic Virus Replication Is Concentration Dependent.
L. M. Guogas, S. M. Laforest, and L. Gehrke (2005)
J. Virol. 79, 5752-5761
   Abstract »    Full Text »    PDF »


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Science. ISSN 0036-8075 (print), 1095-9203 (online)