Structure of hepatitis C virus IRES subdomain IIa

Acta Crystallographica Section D: Biological Crystallography

Volumn 64, Issue 4, 2008, Pages 436-443

  Zhao, Qiang ^a   Han, Qing ^a   Kissinger, Charles R ^a   Hermann, Thomas ^a,b   Thompson, Peggy A ^a  

^a F HOFFMANN LA ROCHE LTD   (Switzerland)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

HCV IRES domain IIa; Magnesium; Metal binding sites; RNA structure; Strontium

Indexed keywords

MAGNESIUM; MANGANESE; METAL; STRONTIUM; VIRUS RNA;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; HEPATITIS C VIRUS; INFORMATION PROCESSING; PROTEIN CONFORMATION; RIBOSOME; VIRUS GENE; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; DATA COLLECTION; GENES, VIRAL; HEPACIVIRUS; MAGNESIUM; MANGANESE; METALS; MODELS, MOLECULAR; PROTEIN CONFORMATION; RIBOSOMES; RNA, VIRAL; STRONTIUM;

HEPATITIS C VIRUS;

EID: 41949111249     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S0907444908002011     Document Type: Article

References (51)

1. Allain, F. H. & Varani, G. (1995). Nucleic Acids Res. 23, 341-350.
2. Baugh, C., Grate, D. & Wilson, C. (2000). J. Mol. Biol. 301, 117-128.
3. Boehringer, D., Theremann, R., Ostareck-Lederer, A., Lewis, J. D. & Stark, H. (2005). Structure, 13, 1695-1706.
4. Brown, E. A., Zhang, H., Ping, L. H. & Lemon, S. M. (1992). Nucleic Acids Res. 20, 5041-5045.
5. 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.
6. Bukh, J., Purcell, R. H. & Miller, R. H. (1992). Proc. Natl Acad. Sci. USA, 89, 4942-4946.
7. Cate, J. H., Hanna, R. L. & Doudna, J. A. (1997). Nature Struct. Biol. 4, 553-558.
8. Chandrasekhar, K. & Malathi, R. (2003). J. Biosci. 28, 547-555.
9. Davidson, F., Simmonds, P., Ferguson, J. C., Jarvis, L. M., Dow, B. C., Follett, E. A., Seed, C. R., Krusius, T., Lin, C. & Medgyesi, G. A. (1995). J. Gen. Virol. 76, 1197-1204.
10. DeLano, W. L. (2002). The PyMOL Molecular Graphics System. Palo Alto, California, USA: DeLano Scientific.
11. Deng, J., Xiong, Y. & Sundaralingam, M. (2001). Proc. Natl Acad. Sci. USA, 98, 13665-13670.
12. Dibrov, S. M., Johnston-Cox, H., Weng, Y. H. & Hermann, T. (2007). Angew. Chem. Int. Ed. Engl. 46, 226-229.
13. Draper, D. E. (2004). RNA, 10, 335-343.
14. Gautheret, D., Konings, D. & Gutell, R. R. (1995). RNA, 1, 807-814.
15. Hermann, T. & Patel, D. J. (1999). J. Mol. Biol. 294, 829-849.
16. Honda, M., Brown, E. A. & Lemon, S. M. (1996). RNA, 2, 955-968.
17. Ji, H., Fraser, C. S., Yu, Y., Leary, J. & Doudna, J. A. (2004). Proc. Natl. Acad. Sci. USA, 101, 16990-16995.
18. Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119.
19. Keift, J. S. & Tinoco, I. J. (1997). Structure, 5, 713-721.
20. Kieft, J. S., Zhou, K., Jubin, R. & Doudna, J. A. (2001). RNA, 7, 194-206.
21. Kieft, J. S., Zhou, K., Jubin, R., Murray, M. G., Lau, J. Y. & Doudna, J. A. (1999). J. Mol. Biol. 292, 513-529.
22. Kikuchi, K., Umehara, T., Fukuda, K., Hwang, J., Kuno, A., Hasegawa, T. & Nishikawa, S. (2003). J. Biochem. (Tokyo), 133, 263-270.
23. Klinck, R., Westhof, E., Walker, S., Afshar, M., Collier, A. & Aboul-Ela, F. (2000). RNA, 6, 1423-1431.
24. Kolupaeva, V. G., Pestova, T. V. & Hellen, C. U. (2000). J. Virol. 74, 6242-6250.
25. Lafuente, E., Ramos, R. & Martinez-Salas, E. (2002). J. Gen. Virol. 83, 1113-1121.
26. Laletina, E., Graifer, D., Malygin, A., Ivanov, A., Shatsky, I. & Karpova, G. (2006). Nucleic Acids Res, 34, 2027-2036.
27. Lavery, R. & Sklenar, H. (1989). J. Biomol. Struct. Dyn. 6, 655-667.
28. Locker, N., Easton, L. E. & Lukavsky, P. J. (2007). EMBO J. 26, 795-805.
29. Lu, H., Li, W., Noble, W. S., Payan, D. & Anderson, D. C. (2004). J. Proteome Res. 3, 949-957.
30. Lukavsky, P. J., Kim, I., Otto, G. A. & Puglisi, J. D. (2003). Nature Struct. Biol. 10, 1033-1038.
31. Lyons, A. J., Lytle, J. R., Gomez, J. & Robertson, H. D. (2001). Nucleic Acids Res. 29, 2535-2541.
32. Mueller, U., Schubel, H., Sprinzl, M. & Heinemann, U. (1999). RNA, 5, 670-677.
33. Otto, G. A. & Puglisi, J. D. (2004). Cell, 119, 369-380.
34. Otwinowski, Z. & Minor, W. (1997). Methods Enzymol. 276, 307-326.
35. Pestova, T. V., Kolupaeva, V. G., Lomakin, I. B., Pilipenko, E. V., Shatsky, I. N., Agol, V. I. & Hellen, C. U. (2001). Proc. Natl Acad. Sci. USA, 98, 7029-7036.
36. Pestova, T. V., Shatsky, I. N., Fletcher, S. P., Jackson, R. J. & Hellen, C. U. (1998). Genes Dev. 12, 67-83.
37. Potterton, E., McNicholas, S., Krissinel, E., Cowtan, K. & Noble, M. (2002). Acta Cryst. D58, 1955-1957.
38. Reynolds, J. E., Kaminski, A., Carroll, A. R., Clarke, B. E., Rowlands, D. J. & Jackson, R. J. (1996). RNA, 2, 867-878.
39. Seth, P. P., Miyaji, A., Jefferson, E. A., Sannes-Lowery, K. A., Osgood, S. A., Propp, S. S., Ranken, R., Massire, C., Sampath, R., Ecker, D. J., Swayze, E. E. & Griffey, R. H. (2005). J. Med. Chem. 48, 7099-7102.
40. Siridechadilok, B., Fraser, C. S., Hall, R. J., Doudna, J. A. & Nogales, E. (2005). Science, 310, 1513-1515.
41. Spahn, C. M., Jan, E., Mulder, A., Grassucci, R. A., Sarnow, P. & Frank, J. (2004). Cell, 118, 465-475.
42. Spahn, C. M., Kieft, J. S., Grassucci, R. A., Penczek, P. A., Zhou, K., Doudna, J. A. & Frank, J. (2001). Science, 291, 1959-1962.
43. Terwilliger, T. C. (2000). Acta Cryst. D56, 965-972.
44. Terwilliger, T. C. & Berendzen, J. (1999). Acta Cryst. D55, 849-861.
45. Tsukiyama-Kohara, K., Iizuka, N., Kohara, M. & Nomoto, A. (1992). J. Virol. 66, 1476-1483.
46. Wadley, L. M. & Pyle, A. M. (2004). Nucleic Acids Res. 32, 6650-6659.
47. Wahl, M. C., Ramakrishnan, B., Ban, C., Chen, X. & Sundaralingam, M. (1996). Acta Cryst. D52, 668-675.
48. Wang, C., Le, S. Y., Ali, N. & Siddiqui, A. (1995). RNA, 1, 526-537.
49. Wang, C., Sarnow, P. & Siddiqui, A. (1993). J. Virol. 67, 3338-3344.
50. Wedekind, J. E. & McKay, D. B. (2003). Biochemistry, 42, 9554-9563.
51. Yu, Y., Ji, H., Doudna, J. A. & Leary, J. A. (2005). Protein Sci. 14, 1438-1446.