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Flexible filamentous virus structures from fiber diffraction

Published online by Cambridge University Press:  29 February 2012

Gerald Stubbs ,
Amy Kendall ,
Michele McDonald ,
Wen Bian ,
Timothy Bowles ,
Sarah Baumgarten ,
Ian McCullough ,
Jian Shi ,
Phoebe Stewart  and
Esther Bullitt
...Show all authors
Gerald Stubbs*
Affiliation:
Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232
Amy Kendall
Affiliation:
Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232
Michele McDonald
Affiliation:
Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232
Wen Bian
Affiliation:
Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232
Timothy Bowles
Affiliation:
Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232
Sarah Baumgarten
Affiliation:
Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232
Ian McCullough
Affiliation:
Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232
Jian Shi
Affiliation:
Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232
Phoebe Stewart
Affiliation:
Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232
Esther Bullitt
Affiliation:
Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02118
David Gore
Affiliation:
BioCAT, Illinois Institute of Technology, Chicago, Illinois 60439
Said Ghabrial
Affiliation:
Plant Pathology Department, University of Kentucky, Lexington, Kentucky 40546
*
a)Author to whom correspondence should be addressed. Electronic mail: [email protected]
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Abstract

Fiber diffraction data have been obtained from Narcissus mosaic virus, a potexvirus from the family Flexiviridae, and soybean mosaic virus (SMV), a potyvirus from the family Potyviridae. Analysis of the data in conjunction with cryo-electron microscopy data allowed us to determine the symmetry of the viruses and to make reconstructions of SMV at 19 Å resolution and of another potexvirus, papaya mosaic virus, at 18 Å resolution. These data include the first well-ordered data ever obtained for the potyviruses and the best-ordered data from the potexviruses, and offer the promise of eventual high resolution structure determinations.

Keywords

fiber diffractioncryo-electron microscopypotyviruspotexvirussoybean mosaic virus
Type
X-Ray Diffraction
Information
Powder Diffraction , Volume 23 , Issue 2 , June 2008 , pp. 113 - 117
Copyright
Copyright © Cambridge University Press 2008

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References

Bernal, J. D. and Fankuchen, I. (1941). “X-Ray and crystallographic studies of plant virus preparations: I. Introduction and preparation of specimens II. Modes of aggregation of the virus particles,” J. Gen. Physiol. JGPLAD 10.1085/jgp.25.1.111 25, 111–165.CrossRefGoogle ScholarPubMed
Bian, W., Wang, H., McCullough, I., and Stubbs, G. (2006). “WCEN: A computer program for initial processing of fiber diffraction patterns,” J. Appl. Crystallogr. JACGAR 39, 752–756.CrossRefGoogle Scholar
Blanch, E. W., Robinson, D. J., Hecht, L., Syme, C. D., Nielsen, K., and Barron, L. D. (2002). “Solution structures of potato virus X and narcissus mosaic virus from raman optical activity,” J. Gen. Virol. JGVIAY 83, 241–246.CrossRefGoogle ScholarPubMed
Bragg, L. and Perutz, M. F. (1952). “The structure of haemoglobin,” Proc. R. Soc. London, Ser. A PRLAAZ 213, 425–435.Google Scholar
Caspar, D. L. D. (1956). “Structure of tobacco mosaic virus: Radial density distribution in the tobacco mosaic virus particle,” Nature (London) NATUAS 177, 928–928.CrossRefGoogle Scholar
Chandrasekaran, R. and Stubbs, G. (2001). “Fibre diffraction,” in International Tables for Crystallography, Vol. F: Crystallography of Biological Macromolecules, edited by Rossman, M. G. and Arnold, E. (Kluwer Academic Publishers, Dordrecht, The Netherlands), pp. 444–450.Google Scholar
Chandrasekaran, R., Radha, A., Lee, E. J., and Zhang, M. (1994). “Molecular architecture of Araban, Galactoglucan and Welan,” Carbohydr. Polym. CAPOD8 25, 235–243.CrossRefGoogle Scholar
Egelman, E. H. (2000). “A robust algorithm for the reconstruction of helical filaments using single-particle methods,” Ultramicroscopy ULTRD6 85, 225–234.CrossRefGoogle ScholarPubMed
Egelman, E. H. (2007). “The iterative helical real space reconstruction method: Surmounting the problems posed by real polymers,” J. Struct. Biol. JSBIEM 157, 83–94.CrossRefGoogle ScholarPubMed
Fauquet, C. M., Mayo, M. A., Maniloff, J., Desselberger, U. and Ball, L. A. (Eds.) (2005). Virus Taxonomy: Eighth Report of the International Committee on Taxonomy of Viruses (Elsevier/Academic Press, London).Google Scholar
Frank, J., Radermacher, M., Penczek, P., Zhu, J., Li, Y., Ladjadj, M., and Leith, A. (1996). “SPIDER and WEB: Processing and visualization of images in 3D electron microscopy and related fields,” J. Struct. Biol. JSBIEM 10.1006/jsbi.1996.0030 116, 190–199.CrossRefGoogle ScholarPubMed
Franklin, R. E. and Holmes, K. C. (1958). “Tobacco mosaic virus: Application of the method of isomorphous replacement to the determination of the helical parameters and radial density distribution,” Acta Crystallogr. ACCRA9 11, 213–220.CrossRefGoogle Scholar
Goodman, R. M., McDonald, J. G., Horne, R. W., and Bancroft, J. B. (1976). “Assembly of flexuous plant viruses and their proteins,” Philos. Trans. R. Soc. London, Ser. B PTRBAE 276, 173–179.Google ScholarPubMed
Gregory, J. and Holmes, K. C. (1965). “Methods of preparing oriented tobacco mosaic virus sols for x-ray diffraction,” J. Mol. Biol. JMOBAK 13, 796–801.CrossRefGoogle Scholar
Harauz, G. and van Heel, M. (1986). “Exact filters for general geometry in three dimensional reconstruction,” Optik (Stuttgart) OTIKAJ 73, 146–156.Google Scholar
Holmes, K. C., Stubbs, G. J., Mandelkow, E., and Gallwitz, U. (1975). “Structure of tobacco mosaic virus at 6.7 Å resolution,” Nature (London) NATUAS 254, 192–196.CrossRefGoogle ScholarPubMed
Kendall, A., Bian, W., Junn, J., McCullough, I., Gore, D., and Stubbs, G. (2007). “Radial density distribution and symmetry of a potexvirus, narcissus mosaic virus,” Virology VIRLAX 357, 158–164.CrossRefGoogle ScholarPubMed
Ludtke, S. J., Baldwin, P. R., and Chiu, W. (1999). “EMAN: Semiautomated software for high-resolution single-particle reconstructions,” J. Struct. Biol. JSBIEM 10.1006/jsbi.1999.4174 128, 82–97.CrossRefGoogle ScholarPubMed
Marvin, D. A. (1998). “Filamentous phage structure, infection and assembly,” Curr. Opin. Struct. Biol. COSBEF 8, 150–158.CrossRefGoogle ScholarPubMed
McDonald, J. G., Beveridge, T. J., and Bancroft, J. B. (1976). “Self-assembly of protein from a flexuous virus,” Virology VIRLAX 69, 327–331.CrossRefGoogle ScholarPubMed
Namba, K., Pattanayek, R., and Stubbs, G. (1989). “Visualization of protein-nucleic acid interactions in a virus: Refined structure of intact tobacco mosaic virus at 2.9 Å resolution by x-ray fiber diffraction,” J. Mol. Biol. JMOBAK 208, 307–325.CrossRefGoogle Scholar
Parker, L., Kendall, A., and Stubbs, G. (2002). “Surface features of potato virus X from fiber diffraction,” Virology VIRLAX 300, 291–295.CrossRefGoogle ScholarPubMed
Parker, L., Kendall, A., Berger, P. H., Shiel, P. J., and Stubbs, G. (2005). “Wheat streak mosaic virus—structural parameters for a potyvirus,” Virology VIRLAX 340, 64–69.CrossRefGoogle ScholarPubMed
Richardson, J. F., Tollin, P., and Bancroft, J. B. (1981). “The architecture of the potexviruses,” Virology VIRLAX 112, 34–39.CrossRefGoogle ScholarPubMed
Tollin, P., Wilson, H. R., Young, D. W., Cathro, J., and Mowat, W. P. (1967). “X-Ray diffraction and electron microscope studies of narcissus mosaic virus, and comparison with potato virus X,” J. Mol. Biol. JMOBAK 26, 353–354.CrossRefGoogle ScholarPubMed
Tollin, P., Wilson, H. R., and Bancroft, J. B. (1980). “Further observations on the structure of particles of potato virus X,” J. Gen. Virol. JGVIAY 49, 407–410.CrossRefGoogle Scholar
Torbet, J. (1987). “Using magnetic orientation to study structure and assembly,” Trends Biochem. Sci. TBSCDB 12, 327–330.CrossRefGoogle Scholar
Varma, A., Gibbs, A. J., Woods, R. D., and Finch, J. T. (1968). “Some observations on the structure of the filamentous particles of several plant viruses,” J. Gen. Virol. JGVIAY 2, 107–114.CrossRefGoogle ScholarPubMed
Wang, H., Planchart, A., and Stubbs, G. (1998). “Caspar carboxylates: The structural basis of tobamovirus disassembly,” Biophys. J. BIOJAU 74, 633–638.CrossRefGoogle ScholarPubMed
Welsh, L. C., Symmons, M. F., Sturtevant, J. M., Marvin, D. A., and Perham, R. N. (1998). “Structure of the capsid of pf3 filamentous phage determined from x-ray fibre diffraction data at 3.1 Å resolution,” J. Mol. Biol. JMOBAK 10.1006/jmbi.1998.2081 283, 155–177.CrossRefGoogle ScholarPubMed
Yamashita, I., Suzuki, H., and Namba, K. (1998a). “Multiple-step method for making exceptionally well-oriented liquid-crystalline sols of macromolecular assemblies,” J. Mol. Biol. JMOBAK 10.1006/jmbi.1998.1710 278, 609–615.CrossRefGoogle ScholarPubMed
Yamashita, I., Hasegawa, K., Suzuki, H., Vonderviszt, F., Mimori-Kiyosue, Y., and Namba, K. (1998b). “Structure and switching of bacterial flagellar filaments studied by x-ray fiber diffraction,” Nat. Struct. Biol. NSBIEW 10.1038/nsb0298-125 5, 125–132.CrossRefGoogle ScholarPubMed
Yang, S., Yu, X., Galkin, V. E., and Egelman, E. H. (2003). “Issues of resolution and polymorphism in single-particle reconstruction,” J. Struct. Biol. JSBIEM 144, 162–171.CrossRefGoogle ScholarPubMed