Virus crystallography

Macromolecular Crystallography: Conventional and high-throughput methods

Volumn 9780198520979, Issue , 2007, Pages

  Fry, Elizabeth E ^a   Abrescia, Nicola G A ^a   Stuart, David I ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Bacteriophage prd1; Blue tongue virus core; Crystallography; Isometric virus structure

Indexed keywords

BACTERIOPHAGES;

BACTERIOPHAGE PRD1; BLUE TONGUE VIRUS CORE; SEPARATE CASE STUDIES; VIRUS CRYSTALLOGRAPHY; VIRUS STRUCTURE;

CRYSTALLOGRAPHY;

EID: 84920752566     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1093/acprof:oso/9780198520979.003.0016     Document Type: Chapter

References (82)

1. Abrescia, N. G., et al. (2004). Insights into assembly from structural analysis of bacteriophage PRD1. Nature 432, 68-74.
2. Anduleit, K., et al. (2005). Crystal lattice as biological phenotype for insect viruses. Protein Science 14, 2741-2743.
3. Arnold, E., et al. (1987). Structure determination of a common cold virus, human rhinovirus 14. Acta Crystallogr. A43, 346-361.
4. Bamford, J. K., et al. (2002). Diffraction quality crystals of PRD1, a 66-MDa dsDNA virus with an internal membrane. J. Struct. Biol. 139, 103-112.
5. Bamford, D. H., Grimes, J. M. and Stuart, D. I. (2005). What does structure tell us about virus evolution? Curr. Opin. Struct. Biol. 15, 655-663.
6. Berman, H. M., et al. (2000). The Protein Data Bank. Nucleic Acids Res. 28, 235-242.
7. Bernal, J. D. and I. Fankuchen (1941). X-ray and crystallographic studies of plant virus preparations. III. J. Gen. Physiol. 25, 111-146.
8. Bricogne, G. (1976). Methods and programs for direct-space exploitation of geometric redundancies. Acta Crystallogr. A 32, 832-847.
9. Brown, J., et al. (2003). A procedure for setting up high throughput nanolitre crystallization experiments II:Crystallization results. J. Appl. Crystallogr. 36, 315-318.
10. Brunger, A. T. (1992). XPLOR Version 3.1. Yale University Press, New Haven and London.
11. Brunger, A. T., et al. (1998). Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905-921.
12. Caspar, D. L. D. and Klug, A. (1962). Physical principles in the construction of regular viruses. Cold. Spring Harbour Symp. Quant. Biol. 27, 12219-12223.
13. CCP4 (1994). The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. D 50, 760-763.
14. CCP4 (1979). The SERC (UK) Collaborative Computing Project No. 4, a Suite of Programs for Protein Crystallography. Daresbury Laboratory, Warrington, WA4 4AD, UK.
15. Chen, Z. G., et al. (1989). Protein-RNA interactions in an icosahedral virus at 3.0 A resolution. Science 245, 154-159.
16. Chiu, W. and Rixon, F. J. (2002). High resolution structural studies of complex icosahedral viruses: a brief overview. Virus Res. 82, 9-17.
17. Cockburn, J. J., et al. (2003). Crystallization of the membrane-containing bacteriophage PRD1 in quartz capillaries by vapour diffusion. Acta Crystallogr. D 59, 538-540.
18. Cockburn, J. J., et al. (2004). Membrane structure and interactions with protein and DNA in bacteriophage PRD1. Nature 432, 122-125.
19. Conway, J. F., et al. (1997). Visualization of a 4-helix bundle in the hepatitis B virus capsid by cryo-electron microscopy. Nature 386, 91-94.
20. Crowfoot, D. and Schmidt, G. M. J. (1945). X-ray crystallographic measurements on a single crystal of a tobacco necrosis virus derivative. Nature 155, 504-505.
21. Cullis, A. F., et al. (1962). The structure of haemoglobin. IX. A threedimensional Fourier synthesis at 5.5A resolution: description of the structure. Proc. R. Soc. London Ser. A. 265, 161-187.
22. Diprose, J. M. (2000). Structural Studies on Orbiviruses. D.Phil. thesis, University of Oxford.
23. Diprose, J. M., et al. (1999). Bluetongue virus: the role of synchrotron radiation. J. Synchrotron Rad. 6, 865-874.
24. Diprose, J. M., et al. (2001). Translocation portals for the substrates and products of a viral transcription complex: the bluetongue virus core. EMBO J. 20, 7229-7239.
25. Dokland, T., et al. (1998). Structure determination of the phiX174 closed procapsid. Acta Crystallogr. D 54, 878-890.
26. Filman, D. J., et al. (1998). Structure determination of echovirus 1. Acta Crystallogr. D 54, 1261-1272.
27. Fourme, R., et al. (2002). Opening the high-pressure domain beyond 2 kbar to protein and virus crystallography-technical advance. Structure (Camb) 10, 1409-1414.
28. Franklin, R. E. (1955). Structure of tobacco mosaic virus. Nature 175, 379-381.
29. Fry, E., Acharya, R. and Stuart, D. (1993). Methods used in the structure determination of foot-and-mouth disease virus. Acta Crystallogr. A 49, 45-55.
30. Fry, E. E., et al. (2003). Crystal structure of Swine vesicular disease virus and implications for host adaptation. J. Virol. 77, 5475-5486.
31. Geerlof, A., et al. (2006). The impact of protein characterization in structural proteomics. Acta Crystallogr. D 62, 1125-1136.
32. Gilbert, R. J., Grimes, J. M. and Stuart, D. I. (2003). Hybrid vigor: hybrid methods in viral structure determination. Adv. Protein Chem. 64, 37-91.
33. Gilliland, G. L., Tung, M. and Ladner, J. E. (2002). The Biological Macromolecule Crystallization Database: procedures and strategies. Acta Crystallogr. D 58, 916-920.
34. Gouet, P., et al. (1999). The highly ordered double-stranded RNA genome of bluetongue virus revealed by crystallography. Cell 97, 481-490.
35. Grimes, J., et al. (1995). The crystal structure of bluetongue virus VP7. Nature 373, 167-170.
36. Grimes, J. M., et al. (1997). An atomic model of the outer layer of the bluetongue virus core derived from X-ray crystallography and electron cryomicroscopy. Structure 5, 885-893.
37. Grimes, J. M., et al. (1998). The atomic structure of the bluetongue virus core. Nature 395, 470-478.
38. Harlos, K. (1992). Micro-bridges for sitting drop crystallisations. J. Appl. Cryst. 25, 536-538.
39. Harrison, S. C., et al. (1978). Tomato bushy stunt virus at 2.9 Å. Nature 276, 368-373.
40. Hendrickson, W. A. (2000). Synchrotron crystallography. Trends Biochem. Sci. 25, 637-643.
41. Hewat, E. A. and Blaas, D. (1996). Structure of a neutralizing antibody bound bivalently to human rhinovirus 2. EMBO J. 15, 1515-1523.
42. Hewat, E. A., Booth, T. F. and Roy, P. (1994). Structure of correctly self-assembled bluetongue virus-like particles. J. Struct. Biol. 112, 183-191.
43. Hewat, E. A., et al. (1997). Structure of the complex of an Fab fragment of a neutralizing antibody with foot-and-mouth disease virus: Positioning of a highly mobile antigenic loop. EMBO J. 16, 1492-1500.
44. Jancarik, J., et al. (2004). Optimum solubility (OS) screening: an efficient method to optimize buffer conditions for homogeneity and crystallization of proteins. Acta Crystallogr. D 60, 1670-1673.
45. Jones, T. A., et al. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110-119.
46. Kabsch, W. (1988). Automatic indexing of rotation diffraction patterns. J. Appl. Cryst. 21, 67-71.
47. Kendrew, J. C., et al. (1960). Structure of myoglobin. A three-dimensional Fourier synthesis at 2A resolution. Nature 185, 422-427.
48. Kleywegt, G. J. and Read, R. J. (1997). Not your average density. Structure 5, 1557-1569.
49. Lea, S. and Stuart, D. (1995). Deconvolution of fully overlapped reflections from crystals of foot-and-mouth disease virus O1 G67. Acta Crystallogr. D 51, 160-167.
50. Lee, K. K. and Johnson, J. E. (2003). Complimentary approaches to structure determination of icosahedral viruses. Curr. Opin. Struct. Biol. 13, 558-569.
51. McCoy, A. J., et al. (2005). Likelihood enhanced fast translation functions. Acta Crystallogr. D 61, 458-464.
52. Miller, S. T., Hogle, J. M. and Filman, D. J. (2001). Ab initio phasing of highsymmetry macromolecular complexes: successful phasing of authentic poliovirus data to 3.0A resolution. J. Mol. Biol. 307, 499-512.
53. Muchmore, S. W., et al. (2000). Automated crystal mounting and data collection for protein crystallography. Structure Fold Des. 8, R243-246.
54. Naitow, H., et al. (1999). A low-resolution structure of rice dwarf virus determined by ab initio phasing. Acta Crystallogr. D 55, 77-84.
55. Naitow, H., et al. (2001). Purification, crystallization and preliminary X-ray analysis of L-A: a dsRNA yeast virus. J. Struct. Biol. 135, 1-7.
56. Nettleship, J. E., et al. (2005). Sample preparation and mass spectrometric characterisation of crystal-derived protein samples. Acta Crystallogr. D 61, 643-645.
57. Otwinoski, Z. (1993). Oscillation data reduction program. In: Data Collection and Processing, Sawyer, L., Isaacs, N. and Bailey, S., eds, pp. 56-62. Daresbury laboratory, SERC, Warrington, UK.
58. Pflugrath, J. W. (1999). The finer things in X-ray diffraction data collection. Acta Crystallogr. D 55, 1718-1725.
59. Pokric, M., et al. (2002). Large area high-resolution CCD-based X-ray detector for macromolecular crystallography. Nucl. Instrum. Meth. A. 477, 166-171.
60. Rayment, I. (1983). Molecular replacement method at low resolution:optimum strategy and intrinsic limitations as determined by calculations on icosahedral virus models. Acta Crystallogr. A 39, 102-116.
61. Reinisch, K. M., Nibert, M. L. and Harrison, S. C. (2000). Structure of the reovirus core at 3.6 A resolution. Nature 404, 960-967.
62. Rossmann, M. G. (1979). Processing oscillation diffraction data from very large unit cells with an automatic convolution technique and profile fitting. J. Appl. Cryst. 12, 225-238.
63. Rossmann, M. G. (1998). From the structures of simple salts to those of sophisticated viruses. Acta Crystallogr. A 54, 716-728.
64. Rossmann, M. and Erickson, J. (1983). Oscillation photography of radiationsensitive crystals using a synchrotron source. J. Appl. Cryst. 16, 629-636.
65. Rossmann, M. G., Bernal, R. and Pletnev, S. V. (2001). Combining electron microscopic with X-ray crystallographic structures. J. Struct. Biol. 136, 190-200.
66. Snell, G., et al. (2004). Automated sample mounting and alignment system for biological crystallography at a synchrotron source. Structure 12, 537-545.
67. SPINE special issue (2006). Structural Proteomics IN Europe. Acta Crystallogr. D 62, 1103-1285.
68. Stanley, W. M. (1935). Isolation of a crystalline protein possessing the properties of tobacco mosaic virus. Science 81, 644-645.
69. Sutton, G., et al. (2004). The nsp9 replicase protein of SARS-coronavirus, structure and functional insights. Structure (Camb) 12, 341-353.
70. Tsao, J., et al. (1992). Structure determination of monoclinic canine parvovirus. Acta Crystallogr. B 48, 75-88.
71. Tsuruta, H., et al. (1998). Imaging RNA and dynamic protein segments with low-resolution virus crystallography: experimental design, data processing and implications of electron density maps. J. Mol. Biol. 284, 1439-1452.
72. Vagin, A. A. and Isupov, M. N. (2001). Spherically averaged phased translation function and its application to the search for molecules and fragments in electron-density maps. Acta Crystallogr. D 57, 1451-1456.
73. Verdaguer, N., et al. (2004). X-ray structure of a minor group human rhinovirus bound to a fragment of its cellular receptor protein. Nat. Struct. Mol. Biol. 11, 429-434.
74. Walter, T. S., et al. (2005). A procedure for setting up high throughput nanolitre crystallization experiments. III. Crystallization workflow for initial screening, automated storage, imaging and optimization. Acta Crystallogr. D 61, 651-657.
75. Walter, T. S., et al. (2003). A procedure for setting up high-throughput nanolitre crystallization experiments. I protocol design and validation. J. Appl. Cryst. 36, 308-314.
76. Wang, B.-C. (1985). Resolution of phase ambiguity in macromolecular crystallography. Method Enzymol. 115, 90-117.
77. Wien, M. W., et al. (1997). Structural studies of poliovirus mutants that overcome receptor defects. Nat. Struct. Biol. 4, 666-674.
78. Wikoff, W. R., Schildkamp, W. and Johnson, J. E. (1997). Increased resolution data from a large unit cell crystal collected at a third-generation synchrotron X-ray source. Acta Crystallogr. D 56, 890-893.
79. Wynne, S. A., et al. (1999). Crystallization of hepatitis B virus core protein shells: determination of cryoprotectant conditions and preliminary X-ray characterization. Acta Crystallogr. D 55, 557-560.
80. Xiao, C., et al. (2001). Interaction of coxsackievirus A21 with its cellular receptor, ICAM-1. J. Virol. 75, 2444-2451.
81. Zheng, Y., Doerschuk, P. C. and Johnson, J. E. (1995). Determination of threedimensional low-resolution viral structure from solution x-ray scattering data. Biophys J. 69, 619-639.
82. Zlotnick, A., et al. (1999). Separation and crystallization of T = 3 and T = 4 icosahedral complexes of the hepatitis B virus core protein. Acta Crystallogr. D 55, 717-720.