Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus

Abstract

The three-dimensional structure of rice dwarf virus was determined to 6.8 Å resolution by single particle electron cryomicroscopy. By integrating the structural analysis with bioinformatics, the folds of the proteins in the double-shelled capsid were derived. In the outer shell protein, the uniquely orientated upper and lower domains are composed of similar secondary structure elements but have different relative orientations from that of bluetongue virus in the same Reoviridae family. Differences in both sequence and structure between these proteins may be important in defining virus–host interactions. The inner shell protein adopts a conformation similar to other members of Reoviridae, suggesting a common ancestor that has evolved to infect hosts ranging from plants to animals. Symmetry mismatch between the two shells results in nonequivalent, yet specific, interactions that contribute to the stability of this large macromolecular machine.

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Figure 1: Structure determination of RDV.
Figure 2: Fold model of the outer shell protein P8.
Figure 3: Fold model of the inner shell protein P3.
Figure 4: Molecular interactions between the shells.

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Acknowledgements

This research has been supported by grants from National Institutes of Health, the Robert Welch Foundation and the National Natural Science Foundation of China. Z.H.Z. is a Pew Scholar in the Biomedical Sciences and a Basil O'Connor Starter Scholar of the March of Dimes Foundation. M.L.B. was supported in part by Baylor Research Advocates for Student. We would like to thank B.V.V. Prasad, M.F. Schmid and M. Baker for their helpful comments on the manuscript. Supplementary animations and 3D VRML models are available at http://ncmi.bcm.tmc.edu/~wjiang/rdv/.

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Correspondence to Wah Chiu.

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