Severe diffraction anisotropy, rotational pseudosymmetry and twinning complicate the refinement of a pentameric coiled-coil structure of NSP4 of rotavirus

Acta Crystallographica Section D: Biological Crystallography

Volumn 68, Issue 11, 2012, Pages 1541-1548

  Chacko, Anita R ^a   Zwart, Peter H ^b   Read, Randy J ^c   Dodson, Eleanor J ^d   Rao, C D ^a   Suguna, Kaza ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d UNIVERSITY OF YORK   (United Kingdom)

Author keywords

data pathology; diffraction anisotropy; rotational pseudosymmetry; twinning

Indexed keywords

GLYCOPROTEIN; NS28 PROTEIN, ROTAVIRUS; TOXIN; VIRUS PROTEIN;

ANISOTROPY; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; ROTAVIRUS; ROTAVIRUS INFECTION; VIROLOGY; X RAY CRYSTALLOGRAPHY;

ANISOTROPY; CRYSTALLOGRAPHY, X-RAY; GLYCOPROTEINS; HUMANS; MODELS, MOLECULAR; ROTAVIRUS; ROTAVIRUS INFECTIONS; TOXINS, BIOLOGICAL; VIRAL NONSTRUCTURAL PROTEINS;

EID: 84867792348     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S090744491203836X     Document Type: Article

References (51)

1. Adams, P. D., Grosse-Kunstleve, R. W., Hung, L.-W., Ioerger, T. R., McCoy, A. J., Moriarty, N. W., Read, R. J., Sacchettini, J. C., Sauter, N. K. & Terwilliger, T. C. (2002). Acta Cryst. D58, 1948-1954.
2. Au, K. S., Mattion, N. M. & Estes, M. K. (1993). Virology, 194, 665-673.
3. Ball, J. M., Tian, P., Zeng, C. Q.-Y.,Morris, A. P. & Estes,M. K. (1996). Science, 272, 101-104.
4. Boshuizen, J. A., Rossen, J.W., Sitaram, C. K., Kimenai, F. F., Simons-Oosterhuis, Y., Laffeber, C., Büller, H. A. & Einerhand, A. W. (2004). J. Virol. 78, 10045-10053.
5. Bowman, G. D., Nodelman, I. M., Levy, O., Lin, S. L., Tian, P., Zamb, T. J., Udem, S. A., Venkataraghavan, B. & Schutt, C. E. (2000). J. Mol. Biol. 304, 861-871.
6. Brooks, C. L., Blackler, R. J., Gerstenbruch, S., Kosma, P., Müller-Loennies, S., Brade, H. & Evans, S. V. (2008). Acta Cryst. D64, 1250-1258.
7. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T. & Warren, G. L. (1998). Acta Cryst. D54, 905-921.
8. Chacko, A. R., Arifullah, M., Sastri, N. P., Jeyakanthan, J., Ueno, G., Sekar, K., Read, R. J., Dodson, E. J., Rao, D. C. & Suguna, K. (2011). J. Virol. 85, 12721-12732.
9. Chacko, A. R., Jeyakanthan, J., Ueno, G., Sekar, K., Rao, C. D., Dodson, E. J., Suguna, K. & Read, R. J. (2012). Acta Cryst. D68, 57-61.
10. Chan, W. K., Au, K. S. & Estes, M. K. (1988). Virology, 164, 435-442.
11. Cohen, G. H. (1997). J. Appl. Cryst. 30, 1160-1161.
12. Dauter, Z., Botos, I., LaRonde-LeBlanc, N. & Wlodawer, A. (2005). Acta Cryst. D61, 967-975.
13. Deepa, R., Durga Rao, C. & Suguna, K. (2007). Arch. Virol. 152, 847-859.
14. Dong, Y., Zeng, C. Q.-Y., Ball, J. M., Estes, M. K. & Morris, A. P. (1997). Proc. Natl Acad. Sci. USA, 94, 3960-3965.
15. Emsley, P. & Cowtan, K. (2004). Acta Cryst. D60, 2126-2132.
16. Estes, M. K., Kang, G., Zeng, C. Q.-Y., Crawford, S. E. & Ciarlet, M. (2001). Novartis Found. Symp. 238, 82-96.
17. Fisher, R. G. & Sweet, R. M. (1980). Acta Cryst. A36, 755-760.
18. French, S. & Wilson, K. (1978). Acta Cryst. A34, 517-525.
19. Guelker, M., Stagg, L., Wittung-Stafshede, P. & Shamoo, Y. (2009). Acta Cryst. D65, 523-534.
20. Horie, Y., Nakagomi, O., Koshimura, Y., Nakagomi, T., Suzuki, Y., Oka, T., Sasaki, S., Matsuda, Y. & Watanabe, S. (1999). Virology, 262, 398-407.
21. Jakobsson, E., Nilsson, J., Källström, U., Ogg, D. & Kleywegt, G. J. (2005). Acta Cryst. F61, 274-278.
22. Krissinel, E. & Henrick, K. (2004). Acta Cryst. D60, 2256-2268.
23. Lebedev, A. A., Vagin, A. A. & Murshudov, G. N. (2006). Acta Cryst. D62, 83-95.
24. Lee, S., Sawaya, M. R. & Eisenberg, D. (2003). Acta Cryst. D59, 2191-2199.
25. Lodowski, D. T., Pitcher, J. A., Capel, W. D., Lefkowitz, R. J. & Tesmer, J. J. (2003). Science, 300, 1256-1262.
26. Mahalanobis, P. C. (1936). Proc. Natl Acad. Sci. USA, 1, 49-55.
27. Matthews, B. W. (1968). J. Mol. Biol. 33, 491-497.
28. McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C. & Read, R. J. (2007). J. Appl. Cryst. 40, 658-674.
29. Mir, K. D., Parr, R. D., Schroeder, F. & Ball, J. M. (2007). Virus Res. 126, 106-115.
30. Mirazimi, A., Nilsson, M. & Svensson, L. (1998). J. Virol. 72, 8705-8709.
31. Newton, K., Meyer, J. C., Bellamy, A. R. & Taylor, J. A. (1997). J. Virol. 71, 9458-9465.
32. O'Brien, G. J., Bryant, C. J., Voogd, C., Greenberg, H. B., Gardner, R. C. & Bellamy, A. R. (2000). Virology, 270, 444-453.
33. Otwinowski, Z. & Minor,W. (1997). Methods Enzymol. 276, 307-326.
34. Padilla, J. E. & Yeates, T. O. (2003). Acta Cryst. D59, 1124-1130.
35. Parr, R. D., Storey, S. M., Mitchell, D. M., McIntosh, A. L., Zhou, M., Mir, K. D. & Ball, J. M. (2006). J. Virol. 80, 2842-2854.
36. Ramadan, M. A. M., Shrive, A. K., Holden, D., Myles, D. A. A., Volanakis, J. E., DeLucas, L. & Greenhough, T. J. (2002). Acta Cryst. D58, 992-1001.
37. Seo, N.-S., Zeng, C. Q.-Y., Hyser, J. M., Utama, B., Crawford, S. E., Kim, K. J., Höök, M. & Estes, M. K. (2008). Proc. Natl Acad. Sci. USA, 105, 8811-8818.
38. Sheriff, S., Hendrickson,W. A. & Smith, J. L. (1987). J. Mol. Biol. 197, 273-296.
39. Strong, M., Sawaya, M. R., Wang, S., Phillips, M., Cascio, D. & Eisenberg, D. (2006). Proc. Natl Acad. Sci. USA, 103, 8060-8065.
40. Taylor, J. A., O'Brien, J. A., Lord, V. J., Meyer, J. C. & Bellamy, A. R. (1993). Virology, 194, 807-814.
41. Tian, P., Ball, J. M., Zeng, C. Q.-Y. & Estes, M. K. (1996). J. Virol. 70, 6973-6981.
42. Tian, P., Hu, Y., Schilling, W. P., Lindsay, D. A., Eiden, J. & Estes, M. K. (1994). J. Virol. 68, 251-257.
43. Winn, M. D. et al. (2011). Acta Cryst. D67, 235-242.
44. Xu, A., Bellamy, A. R. & Taylor, J. A. (2000). EMBO J. 19, 6465-6474.
45. Yeates, T. O. (1988). Acta Cryst. A44, 142-144.
46. Yeates, T. O. (1997). Methods Enzymol. 276, 344-358.
47. Yu, F., Song, A., Xu, C., Sun, L., Li, J., Tang, L., Yu, M., Yeates, T. O., Hu, H. & He, J. (2009). Acta Cryst. D65, 212-219.
48. Zagotta, W. N., Olivier, N. B., Black, K. D., Young, E. C., Olson, R. & Gouaux, J. E. (2003). Nature (London), 425, 200-205.
49. Zhang, M., Monzingo, A. F., Segatori, L., Georgiou, G. & Robertus, J. D. (2004). Acta Cryst. D60, 1512-1518.
50. Zwart, P. H., Grosse-Kunsteleve, R. W. & Adams, P. D. (2005). CCP4 Newsl. 42, contribution 10.
51. Zwart, P. H., Grosse-Kunstleve, R. W., Lebedev, A. A., Murshudov, G. N. & Adams, P. D. (2008). Acta Cryst. D64, 99-107.