The refined crystal structure of cowpea mosaic virus at 2.8 Å resolution

Virology

Volumn 265, Issue 1, 1999, Pages 20-34

  Lin, Tianwei ^a   Chen, Zhongguo ^b   Usha, Ramakrishnan ^b   Stauffacher, Cynthia V ^b   Dai, Jin Bi ^b   Schmidt, Tim ^b   Johnson, John E ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b PURDUE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

IMMUNOGLOBULIN F(AB) FRAGMENT;

ARTICLE; CRYSTAL STRUCTURE; MOSAIC VIRUS; NONHUMAN; PICORNAVIRUS; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DOMAIN; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; VIRUS CAPSID;

COWPEA MOSAIC VIRUS; MIRIDAE; PICORNAVIRIDAE; RNA VIRUSES;

EID: 0033527898     PISSN: 00426822     EISSN: None     Source Type: Journal    
DOI: 10.1006/viro.1999.0038     Document Type: Article

References (52)

1. Ahlquist P., Dasqupta R., Kaesberg P. Nucleotide sequence of brome mosaic virus genome and its implication for virus replication. J. Mol. Biol. 172:1984;369-383.
2. Brunger A. T. X-PLOR Version 3.1. A system for X-ray crystallography and NMR. 1992;Yale University Press, New Haven.
3. Brunger A. T., Krukowski A., Erickson J. W. Slow-cooling protocols for crystallographic refinement by simulating annealing. Acta Crystallogr. A. 46:1990;585-593.
4. Brunger A. T., Rice L. M. Crystallographic refinement by simulated annealing: methods and applications. Methods Enzymol. 277:1997;243-269.
5. Caspar D. L. D., Klug A. Physical principles in the construction of regular viruses. Cold Spring Harb. Symp. Quant. Biol. 27:1962;1-24.
6. Chandrasekar V., Johnson J. E. The structure of tobacco ringspot virus: a link in the evolution of capsids in the picornavirus superfamily. Structure. 6:1998;157-171.
7. Chen Z., Stauffacher C., Li Y., Schmidt T., Bomu W., Kamer G., Shanks M., Lomonossoff G., Johnson J. E. Protein-RNA interactions in an icosahedral virus at 3.0 Å resolution. Science. 245:1989;154-159.
8. Chen Z., Stauffacher C., Schmidt T., Fisher A., Johnson J. E. RNA packaging in bean pod mottle virus. Margo A., Briton A., Heinz F. X. New Aspects of Positive-Strand RNA Viruses. 1990;218-226 American Society for Microbiology, Washington.
9. Ferrin T. E., Huang C. C., Jarvis L. E., Langridge R. The MIDAS display system. J. Mol. Graph. 9:1988;13-27.
10. Franssen H., Leunissen J., Goldbach R., Lomonossoff G. P., Zimmern D. Homologous sequences in the non-structural proteins from cowpea mosaic virus and picornaviruses. EMBO J. 3:1984;855-861.
11. Hogle J. M., Chow M., Filman D. J. Three-dimensional structure of poliovirus at 2.9 Å resolution. Science. 229:1985;1358-1365.
12. Huang C. C., Petterson E. F., Klein T. E., Ferrin T. E., Langridge R. Conic: a fast renderer for space-filling molecules with shadows. J. Mol. Graph. 9:1991;230-236.
13. Johnson J. E. Averaging of electron density map. Acta Crystallogr. B. 34:1978;575-577.
14. Johnson J. E., Akimoto T., Suck D., Rayment I., Rossmann M. G. The structure of southern bean mosaic virus at 22.5 Å resolution. Virology. 75:1976;394-400.
15. Johnson J. E., Harrington M. Antibody binding to cowpea mosaic virus in the crystalline state. Laver W., Air G. The Immune Recognition of Protein Antigens. 1985;169-173 Cold Spring Harbor Press, Cold Spring Harbor.
16. Johnson J. E., Hollingshead C. Crystallographic studies of cowpea mosaic virus by electron microscopy and X-ray diffraction. J. Ultrastruct. Res. 74:1981;223-231.
17. Johnson K. E., Christian P. D. The novel genome organization of the insect picorna-like virus Drosophila C virus suggests this virus belongs to a previously undescribed virus family. J. Gen. Virol. 79:1998;191-203.
18. Jones T. A., Kjeldgaard M. Electron density map interpretation. Methods Enzymol. 277:1997;173-208.
19. Jones T. A., Zou J. Y., Cowan S. W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A. 47:1991;110-119.
20. Kabsch W., Sander S. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:1983;2577-2637.
21. Kraulis P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:1991;946-950.
22. Kridl J. C., Bruening G. Comparison of capsids and nucleocapsids from cowpea mosaic virus-infected cowpea protoplasts and seedlings. Virology. 129:1983;369-380.
23. Laskowski R. W., MacArthur M. W., Moss D. S., Thornton J. M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26:1993;345-364.
24. Lewis J. K., Bothner B., Smith T. J., Siuzdak G. Antiviral agent blocks breathing of the common cold virus. Proc. Natl. Acad. Sci. USA. 95:1998;6774-6778.
25. Lomonossoff G. P., Johnson J. E. The synthesis and structure of comovirus capsids. Prog. Biophys. Mol. Biol. 55:1991;107-137.
26. Lomonossoff G. P., Shanks M. The nucleotide sequence of cowpea mosaic virus B RNA. EMBO J. 2:1983;2253-2258.
27. Natarajan P., Johnson J. E. Molecular packing in virus crystals: geometry, chemistry, and biology. J. Struct. Biol. 121:1998;295-305.
28. Porta C., Wang G., Cheng H., Chen Z., Baker T. S., Johnson J. E. Direct imaging of interactions between an icosahedral virus and conjugate F(ab) fragments by cryoelectron microscopy and X-ray crystallography. Virology. 204:1994;777-788.
29. Rossmann M. G. Processing oscillation diffraction data for very large unit cells with an automatic convolution technique and profile fitting. J. Appl. Crystallogr. 12:1979;225-238.
30. Rossmann M. G. The canyon hypothesis: hiding the host cell receptor attachment site on a viral surface from immune surveillance. J. Biol. Chem. 264:1989;14587-14590.
31. Rossmann M. G., Arnold E., Erickson J. W., Frankenberger E. A., Griffith J. P., Hecht H.-J., Johnson J. E., Kamer G., Luo M., Mosser A. G., Ruecker R. R., Sherry B., Vriend G. Structure of a human common cold virus and functional relationship to the other picornaviruses. Nature. 317:1985;145-153.
32. Rossmann M. G., Blow D. M. The detection of sub-units within the crystallographic asymmetric unit. Acta Crystallogr. C. 15:1962;24-30.
33. Rossmann M. G., Johnson J. E. Icosahedral RNA virus structure. Ann. Rev. Biochem. 58:1989;533-573.
34. Rossmann M. G., Leslie A. G. W., Abdel-Meguid S. S., Tsukihara T. Processing and post-refinement of oscillation camera data. J. Appl. Crystallogr. 12:1979;570-581.
35. Ruecker R. R. Picornaviruses and their replication. Fields B. N. Virology. 1985;705-738 Raven Press, New York.
36. Schmidt T., Johnson J. E., Phillips W. E. The spherically averaged structures of cowpea mosaic virus components by X-ray solution scattering. Virology. 127:1983;65-73.
37. Sehgal O. P. Sobemoviruses. Singh P. R., Singh U. S., Kohomta K. Pathogenesis and Host Specificity in Plant Disease: Histopathological, Biochemical, Genetic, and Molecular Bases. 1995;115-128 Pergamon.
38. Siler D. J., Babcock J., Bruening G. Electrophoretic mobility and enhanced infectivity of a mutant cowpea mosaic virus. Virology. 71:1976;560-567.
39. Silva A. M., Rossmann M. G. Refined structure of southern bean mosaic virus at 2.9Å resolution. J. Mol. Biol. 197:1987;69-87.
40. Smith T. J., Baker T. Picornaviruses: epitopes, canyons, and pockets. Adv. Virus Res. 52:1999;1-23.
41. Smith T. J., Chase E. S., Schmidt T. J., Olson N. H., Baker T. S. Neutralizing antibody to human rhinovirus 14 penetrates the receptor-binding canyon. Nature. 383:1996;350-354.
42. Smith T. J., Kremer M. J., Luo M., Vriend G., Arnold E., Kamer G., Rossmann M. G., McKinlay M. A., Diana G. D., Otto M. J. The site of attachment in human rhinovirus 14 for antiviral agents that inhibit uncoating. Science. 233:1986;1286-1293.
43. Speir J. A., Munshi S., Wang G., Baker T. S., Johnson J. E. Structure of the native and swollen forms of cowpea chlorotic mottle virus determined by X-ray crystallography and cryo-electron microscopy. Structure. 3:1995;63-78.
44. Stauffacher C. V., Usha R., Harrington M., Schmidt T., Hosur M., Johnson J. E. The structure of cowpea mosaic virus at 3.5Å resolution. Moras D., Drenth J., Strandberg B., Suck D., Wilson K. Crystallography in Molecular Biology. 1987;293-308 Plenum, New York.
45. Tate J. G., Liljas L., Scotti P., Christian P., Lin T., Johnson J. E. The crystal structure of cricket paralysis virus provides the first view of a new virus family. Nat. Struct. Biol. 6:1999;765-774.
46. Tong L., Rossmann M. G. The locked rotation function. Acta Crystallogr. A. 46:1990;783-792.
47. Tong L., Rossmann M. G. Rotation function calculation with GLRF program. Methods Enzymol. 276:1997;594-611.
48. Usha R., Johnson J., Moras D., Thierry J., Fourme R., Kahn R. Macromolecular crystallography with synchrotron radiation: collection and processing data from crystals with a very large unit cell. J. Appl. Crystallogr. 17:1984;147-153.
49. van Wezenbeek P., Verver J., Harmsen J., Vos P., van Kammen A. Primary structure and gene organization of the middle component RNA of cowpea mosaic virus. EMBO J. 2:1983;941-946.
50. 31P nuclear magnetic resonance studies of cowpea mosaic virus B-RNA: detection and exchange of polyamines and dynamics of the RNA. Virology. 141:1985;43-50.
51. Wang G. J., Porta C., Chen Z. G., Baker T. S., Johnson J. E. Identification of a Fab interaction footprint site on an icosahedral virus by cryoelectron and X-ray crystallography. Nature. 355:1992;275-278.
52. White J. M., Johnson J. E. Crystalline cowpea mosaic virus. Virology. 101:1980;319-324.