Crystal structure of turnip yellow mosaic virus

Nature Structural Biology

Volumn 3, Issue 9, 1996, Pages 771-781

  Canady, Mary A ^a   Larson, Steven B ^a   Day, John ^a   McPherson, Alexander ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CAPSID PROTEIN; HISTIDINE; PROTEIN SUBUNIT; VIRUS PROTEIN; VIRUS RNA;

ARTICLE; CRYSTAL STRUCTURE; NONHUMAN; PRIORITY JOURNAL; PROTEIN RNA BINDING; PROTEIN STRUCTURE; RNA CONFORMATION; TURNIP YELLOW MOSAIC VIRUS; VIRUS CAPSID;

AMINO ACID SEQUENCE; CAPSID; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; RNA, VIRAL; TYMOVIRUS;

EID: 0029774740     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsb0996-771     Document Type: Article

References (54)

1. Hirth. L & Givord, L Tymoviruses. In The Plant Viruses (ed. R. Koenig) 3, 163-212 (Plenum, New York, 1988).
2. Morch, M.D., Boyer, J.C. & Haenni A.L. Overlapping open reading frames revealed by complete nucleotide sequencing of turnip yellow mosaic virus genomic RNA. Nuc. Acids Res. 16, 6157-6173 (1988).
3. Pinck, M., Yot, P., Chapeville, F. & Duranton, H.M. Enzymatic binding of valine to the 3′ end of TYMV-RNA Nature 226, 954-956 (1970).
4. Haenni, A.L., Prochiantz, A., Bernard, O. & Chapeville, F. TYMV valyl-RNA as an amino-acid donor in protein biosynthesis. Nature new Biol. 241, 166-168 (1973).
5. Giége R., Florentz, C. S Dreher, T.W. The TYMV tRNA-like structure. Biochimie 75, 569-582 (1993).
6. Matthews, R.E.F. Plant Virology 231-237 (Academic Press, Inc., New York; 1991).
7. Mutombo, K., Michels, B., Ott, H., Cerf, R. & Witz, J. The thermal stability and decapsidation mechanism of tymoviruses: A differential calorimetric study. Biochimie 75, 667-674 (1993).
8. Klug, A., Longley, W. & Leberman, R. Arrangement of protein subunits and the distribution of nucleic acid in turnip yellow mosiac virus. I. X-ray diffraction studies. J. mol. Biol. 15, 315-343 (1966).
9. Finch, J.T. & Klug, A. Arrangement of protein subunits and the distribution of nucleic acid in turnip yellow mosaic virus. II. Electron microscopic studies. J. Mol. Biol. 15, 344-64 (1966).
10. Jacrot, B., Chauvin, C. & Witz, J. Comparative neutron small-angle scattering study of small spherical RNA Viruses. Nature 266, 417-421 (1977).
11. Rubio-Huertos, M., Vela, A. & Lopez-Abella D. Crystalline arrays of spherical particles in turnip yellow mosaic virus-infected cells. Virology 32, 438-444 (1967).
12. Markham, R. & Smith, K.M. Studies on the virus of turnip yellow mosaic. Parasitology 39, 330-343 (1949).
13. Chapman, M.S. & Rossmann, M.G. Comparison of surface properties of picornaviruses: Strategies for hiding the receptor site from immune surveillance. Virology 195, 745-756 (1993).
14. Mellema, I.E. & Amos, LA. Three-dimensional image reconstruction of turnip yellow mosaic virus. J. Mol. Biol. 72, 819-822 (1972).
15. Speir, J.A., Munshi, S., Wang, G., Baker, T.S. & Johnson, J.E. Structures of the native and swollen forms of cowpea chlorotic mottle virus determined by X-ray crystallography and cryo-electron microscopy. Structure 3, 63-78 (1995).
16. Sheriff, S.. Hendrickson, W.A. & Smith, J.L. Structure of myohemerythrin in the azidomet state at 1.7/1.3 Å resolution. J. Mol. Biol. 197, 273-296 (1987).
17. Kaper, J.M. The Chemical basis of virus structure, dissociation, and assembly (North-Holland Publishing Company, Amsterdam; 1975).
18. Peter, R., Stehelin, D., Reinbolt, J., Collot, D. & Duranton, H. Primary structure of turnip yellow mosaic virus coat protein. Virology 49, 615-617 (1972).
19. Chelvanayagam, G., Heringa, J. & Argos, P. Anatomy and evolution of proteins displaying the viral capsid jellyroll topology. J. Mol. Biol. 228 220-242 (1992).
20. Nicholls, A., Sharp, K. & Honig, B. Protein folding and association - insights from the interfacial and therrfiodynamic properties of hydrocarbons. Proteins 11, 281-296 (1991).
21. Witz, J., Timmins, P.A. & Adrian, M. Organization of turnip yellow mosaic virus investigated by neutron small angle scattering at 80 K: An intermediate state preceding decapsidation of the virion? Proteins 17, 223-231 (1993).
22. Pleij, C.W., Eecen, H.G., Bosch, L. & Mandel, M. The formation of fast-sedimenting turnip yellow mosaic virus RNA: Structural rearrangement inside the capsid. Virology 76, 781-786 (1977).
23. 31P nuclear magnetic resonance spectroscopy. Virology 146, 213-220 (1985).
24. Rohozinski, J. & Hancock, J. M. Do light-induced pH changes within the chloroplast drive turnip yellow mosaic virus assembly? J. Gen. Virol. 77, 163-165 (1996).
25. Matthews, R.E.F. & Witz, J. Uncoating of turnip yellow mosaic virus RNA in vivo. Virology 144, 318-327 (1985).
26. Adrian, M., Timmins, P.A. & Witz, J. In vitro decapsidation of turnip yellow mosaic virus investigated by cryo-electron microscopy: a model for the decapsidation of a small isometric virus. J. Gen. Virol. 73, 2079-2083 (1992).
27. Keeling, J. & Matthews, R.E.F. Mechanism for release of RNA from turnip yellow mosaic virus at high pH. Virology 119, 214-218 (1982).
28. Katouzian-Safadi M. & Berthet-Colominas, C. Evidence for the presence of a hole in the capsid of turnip yellow mosaic virus after RNA release by freezing and thawing. Eur. J. Biochem. 137, 47-55 (1983).
29. Quesniaux, V, Jaegle, M. & Van Regenmortel, M.H.V. Immunochemical studies of turnip yellow mosaic virus III. Localization of two viral epitopes in residues 57-64 and 183-189 of the coat protein. Bioch. et Bioph. Acta 743, 226-231 (1983).
30. Quesniaux, V., Briand, J.P. & Van Regenmortel, M.H.V. Immunochemical studies of turnip yellow mosaic virus - II. Localization of a viral epitope in the N-terminal residues of the coat protein. Molec. Immun. 20, 179-185 (1983).
31. Roivainen, M., Piirainen, L., Rysä, T., Nārvānen, A. & Hovi, T. An immunodominant N-terminal region of VP1 protein of poliovirion that is buried in crystal structure can be exposed in solution. Virology 195, 762-765 (1993).
32. Yafal, A.G., Kaplan, G., Racaniello, V.R. & Hogle, J.M. Characterization of poliovirus conformational alteration mediated by soluble cell receptors. Virology 197, 501-515 (1993).
33. Cheng, R.H. et al. Functional implications of quasi-equivalence in a T=3 icosahedral animal virus established by cryo-electron microscopy and X-ray crystallography. Structure 2, 271-282 (1994).
34. Tsao, J. et al. & Parrish, C.R. Three dimensional structure of canine parvovirus and its functional implications. Science 251, 1456-1464 (1991).
35. Langeveld, J.P.M. et al. B-cell epitopes of canine parvovirus: Distribution on the primary structure and exposure on the viral surface. J. Virol. 68, 4506-4513 (1994).
36. Ehresmann, B., Briand, J.P., Reinbolt, J. & Witz, J. Identification of binding sites of turnip yellow mosaic virus protein and RNA induced in situ. Eur. J. Biochem. 108, 123-129 (1980).
37. Chen, Z. et al. & Johnson, J.E. Protein-RNA interactions in an icosahedral virus at 3.0 Å resolution. Science 245, 154-159 (1989).
38. Larson, S.B. et al. Double helical RNA in satellite tobacco mosaic virus. Nature 361, 179-182 (1993).
39. Fisher, A.J. & Johnson, J.E. Ordered duplex RNA controls capsid architecture in an icosahedral animal virus. Nature 361, 176-179 (1993).
40. Wery, J.P., Reddy, V.S., Hosur, M.V. & Johnson, J.E. The refined three-dimensional structure of an insect virus at 2.8 Å resolution. J. mol. Biol. 235, 565-586 (1994).
41. Bottcher, B. & Crowther, R.A. Difference imaging reveals ordered regions of RNA in turnip yellow mosaic virus. Structure 4, 387-394 (1996).
42. Hanna, M. & Szostak, J.W. Suppression of mutations in the core of the Tetrahymena ribozyme by spermidine, ethanol and by substrate stabilization. Nuc. Acids Res. 22, 5326-5331 (1994).
43. Canady, M.A., Day, J. & McPherson, A. Preliminary X-ray diffraction analysis of crystals of turnip yellow mosaic virus (TYMV). Proteins 21, 78-81 (1995).
44. McPherson, A. The growth and preliminary investigation of protein and nucleic acid crystals for X-ray diffraction. In Methods of Biochemical analysis (ed. D. Glick) 249-345 (John Wiley S, Sons, New York, 1976).
45. Otwinowski, Z. Oscillation Data Reduction Program. In Proceedings of the CCP4 Study Weekend: Data Collection and Processing, 22-30 January, (L. Sawyer, N. Isaacs & S. Bailey, compl.) 56-62 (SERC Daresbury Laboratory, England, 1993).
46. Minor, W. XDISPLAYF Program (Purdue University, West Lafayette, Indiana, 1993).
47. Brünger, A.T. X-PLOR Version 3.1. A system for X-ray Crystallography and NMR (Yale University Press, New Haven, 1992).
48. Larson, S.B. et al. Three dimensional structure of satellite tobacco mosaic virus at 2.9 Å resolution. J. Mol. Biol. 21, 375-391 (1993).
49. Bricogne, G. Methods and programs for direct-space exploitation of geometrical redundancies. Acta Crystallogr. A 32, 832-846 (1976).
50. Furey, W. Abstract, American Crystallographic Association, Series 2 (18) 73 (1990).
51. Jones, A.T. & Kjeldgaard, M. "O" Manual, version 5.4 (Uppsala University, Sweden and Aarhus University, Denmark, 1990).
52. Kraulis, P.J. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. appl. Cryst. 24, 945-950 (1991).
53. Evans, S.V. SETOR: hardware lighted three-dimensional solid model representations of macromolecules. J. Molec. Graphics 11, 134-138 (1993).
54. Laskowski, R.A, Macarthur, M.W., Moss, D.S. & Thornton, J.M. Procheck - A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291 (1993).