X-ray structures of eIF5B and the eIF5B-eIF1A complex: The conformational flexibility of eIF5B is restricted on the ribosome by interaction with eIF1A

Acta Crystallographica Section D: Biological Crystallography

Volumn 70, Issue 12, 2014, Pages 3090-3098

  Zheng, Aiping ^a,b   Yu, Jian ^a   Yamamoto, Reo ^a   Ose, Toyoyuki ^a   Tanaka, Isao ^a   Yao, Min ^a  

^a HOKKAIDO UNIVERSITY   (Japan)

^b UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

Author keywords

eIF5B; eIF5B eIF1A complex

Indexed keywords

ARCHAEA; EUKARYOTA;

EUKARYOTIC INITIATION FACTOR-5B; EUKARYOTIC PEPTIDE INITIATION FACTOR-1A; INITIATION FACTOR; INITIATION FACTOR 1; SACCHAROMYCES CEREVISIAE PROTEIN;

CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; PROTEIN CONFORMATION; RIBOSOME; SACCHAROMYCES CEREVISIAE; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; EUKARYOTIC INITIATION FACTOR-1; EUKARYOTIC INITIATION FACTORS; MODELS, MOLECULAR; PROTEIN CONFORMATION; RIBOSOMES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 84916934849     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S1399004714021476     Document Type: Article

References (52)

1. Acker, M. G., Shin, B.-S., Dever, T. E. and Lorsch, J. R. (2006). J. Biol. Chem. 281, 8469-8475.
2. Acker, M. G., Shin, B.-S., Nanda, J. S., Saini, A. K., Dever, T. E. and Lorsch, J. R. (2009). J. Mol. Biol. 385, 491-506.
3. Afonine, P. V., Grosse-Kunstleve, R. W., Echols, N., Headd, J. J., Moriarty, N. W., Mustyakimov, M., Terwilliger, T. C., Urzhumtsev, A., Zwart, P. H. and Adams, P. D. (2012). Acta Cryst. D68, 352-367.
4. Allen, G. S., Zavialov, A., Gursky, R., Ehrenberg, M. and Frank, J. (2005). Cell, 121, 703-712.
5. Battiste, J. L., Pestova, T. V., Hellen, C. U. T. and Wagner, G. (2000). Mol. Cell, 5, 109-119.
6. Boileau, G., Butler, P., Hershey, J. W. and Traut, R. R. (1983). Biochemistry, 22, 3162-3170.
7. Bricogne, G., Blanc, E., Brandl, M., Flensburg, C., Keller, P., Paciorek, W., Roversi, P., Sharff, A., Smart, O. S., Vonrhein, C. and Womack, T. O. (2011). AutoBUSTER. Cambridge: Global Phasing Ltd.
8. Brunger, A. T. (2007). Nature Protoc. 2, 2728-2733.
9. Carter, A. P., Clemons, W. M., Brodersen, D. E., Morgan-Warren, R. J., Hartsch, T., Wimberly, B. T. and Ramakrishnan, V. (2001). Science, 291, 498-501.
10. Caserta, E., Tomsic, J., Spurio, R., La Teana, A., Pon, C. L. and Gualerzi, C. O. (2006). J. Mol. Biol. 362, 787-799.
11. Choi, S. K., Lee, J. H., Zoll, W. L., Merrick, W. C. and Dever, T. E. (1998). Science, 280, 1757-1760.
12. Choi, S. K., Olsen, D. S., Roll-Mecak, A., Martung, A., Remo, K. L., Burley, S. K., Hinnebusch, A. G. and Dever, T. E. (2000). Mol. Cell. Biol. 20, 7183-7191.
13. Cummings, H. S. and Hershey, J.W. B. (1994). J. Bacteriol. 176, 198-205.
14. Eiler, D., Lin, J., Simonetti, A., Klaholz, B. P. and Steitz, T. A. (2013). Proc. Natl Acad. Sci. USA, 110, 15662-15667.
15. Emsley, P., Lohkamp, B., Scott, W. G. and Cowtan, K. (2010). Acta Cryst. D66, 486-501.
16. Fernández, I. S., Bai, X.-C., Hussain, T., Kelley, A. C., Lorsch, J. R., Ramakrishnan, V. and Scheres, S. H.W. (2013). Science, 342, 1240585.
17. Fringer, J. M., Acker, M. G., Fekete, C. A., Lorsch, J. R. and Dever, T. E. (2007). Mol. Cell. Biol. 27, 2384-2397.
18. Guillon, L., Schmitt, E., Blanquet, S. and Mechulam, Y. (2005). Biochemistry, 44, 15594-15601.
19. Hoffman, D. W. and Li, W. (2001). Protein Sci. 10, 2426-2438.
20. Jackson, R. J., Hellen, C. U. T. and Pestova, T. V. (2010). Nature Rev. Mol. Cell Biol. 11, 113-127.
21. Kabsch, W. (2010). Acta Cryst. D66, 125-132.
22. Kolakofsky, D., Ohta, T. and Thach, R. E. (1968). Nature (London), 220, 244-247.
23. Krafft, C., Diehl, A., Laettig, S., Behlke, J., Heinemann, U., Pon, C. L., Gualerzi, C. O. and Welfle, H. (2000). FEBS Lett. 471, 128-132.
24. Laalami, S., Sacerdot, C., Vachon, G., Mortensen, K., Sperling- Petersen, H. U., Cenatiempo, Y. and Grunberg-Manago, M. (1991). Biochimie, 73, 1557-1566.
25. Lee, J. H., Choi, S. K., Roll-Mecak, A., Burley, S. K. and Dever, T. E. (1999). Proc. Natl Acad. Sci. USA, 96, 4342-4347.
26. Leibundgut, M., Frick, C., Thanbichler, M., Böck, A. and Ban, N. (2005). EMBO J. 24, 11-22.
27. Lucas-Lenard, J. (1971). Annu. Rev. Biochem. 40, 409-448.
28. Marintchev, A., Kolupaeva, V. G., Pestova, T. V. and Wagner, G. (2003). Proc. Natl Acad. Sci. USA, 100, 1535-1540.
29. Marshall, R. A., Aitken, C. E. and Puglisi, J. D. (2009). Mol. Cell, 35, 37-47.
30. Moreno, J. M., Drskjotersen, L., Kristensen, J. E., Mortensen, K. K. and Sperling-Petersen, H. U. (1999). FEBS Lett. 455, 130-134.
31. Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F. and Vagin, A. A. (2011). Acta Cryst. D67, 355-367.
32. Myasnikov, A. G., Marzi, S., Simonetti, A., Giuliodori, A. M., Gualerzi, C. O., Yusupova, G., Yusupov, M. and Klaholz, B. P. (2005). Nature Struct. Mol. Biol. 12, 1145-1149.
33. Nomura, N., Honda, T., Baba, K., Naganuma, T., Tanzawa, T., Arisaka, F., Noda, M., Uchiyama, S., Tanaka, I., Yao, M. and Uchiumi, T. (2012). Proc. Natl Acad. Sci. USA, 109, 3748-3753.
34. Olsen, D. S., Savner, E. M., Mathew, A., Zhang, F., Krishnamoorthy, T., Phan, L. and Hinnebusch, A. G. (2003). EMBO J. 22, 193-204.
35. Passmore, L. A., Schmeing, T. M., Maag, D., Applefield, D. J., Acker, M. G., Algire, M. A., Lorsch, J. R. and Ramakrishnan, V. (2007). Mol. Cell, 26, 41-50.
36. Pestova, T. V., Borukhov, S. I. and Hellen, C. U. T. (1998). Nature (London), 394, 854-859.
37. Pestova, T. V., Lomakin, I. B., Lee, J. H., Choi, S. K., Dever, T. E. and Hellen, C. U. T. (2000). Nature (London), 403, 332-335.
38. Roll-Mecak, A., Cao, C., Dever, T. E. and Burley, S. K. (2000). Cell, 103, 781-792.
39. Sette, M., van Tilborg, P., Spurio, R., Kaptein, R., Paci, M., Gualerzi, C. O. and Boelens, R. (1997). EMBO J. 16, 1436-1443.
40. Shiba, K., Ito, K., Nakamura, Y., Dondon, J. and Grunberg-Manago, M. (1986). EMBO J. 5, 3001-3006.
41. Shin, B. S., Maag, D., Roll-Mecak, A., Arefin, M. S., Burley, S. K., Lorsch, J. R. and Dever, T. E. (2002). Cell, 111, 1015-1025.
42. Simonetti, A., Marzi, S., Billas, I. M., Tsai, A., Fabbretti, A., Myasnikov, A. G., Roblin, P., Vaiana, A. C., Hazemann, I., Eiler, D., Steitz, T. A., Puglisi, J. D., Gualerzi, C. O. and Klaholz, B. P. (2013). Proc. Natl Acad. Sci. USA, 110, 15656-15661.
43. Simonetti, A., Marzi, S., Fabbretti, A., Hazemann, I., Jenner, L., Urzhumtsev, A., Gualerzi, C. O. and Klaholz, B. P. (2013). Acta Cryst. D69, 925-933.
44. Simonetti, A., Marzi, S., Myasnikov, A. G., Fabbretti, A., Yusupov, M., Gualerzi, C. O. and Klaholz, B. P. (2008). Nature (London), 455, 416-420.
45. Sperling-Petersen, H. U., Moreno, J. M. P., Dyrskjotersen, L., Kristensen, J. E. and Mortensen, K. K. (1999). FEBS Lett. 455, 130-134.
46. Vagin, A. and Teplyakov, A. (2010). Acta Cryst. D66, 22-25.
47. Wei, C.-L., Kainuma, M. and Hershey, J. W. (1995). J. Biol. Chem. 270, 22788-22794.
48. Weissbach, H. and Ochoa, S. (1976). Annu. Rev. Biochem. 45, 191-216.
49. Weisser, M., Voigts-Hoffmann, F., Rabl, J., Leibundgut, M. and Ban, N. (2013). Nature Struct. Mol. Biol. 20, 1015-1017.
50. Winn, M. D., Isupov, M. N. and Murshudov, G. N. (2001). Acta Cryst. D57, 122-133.
51. Yao, M., Zhou, Y. and Tanaka, I. (2006). Acta Cryst. D62, 189-196.
52. Zheng, A., Yamamoto, R., Sokabe, M., Tanaka, I. and Yao, M. (2011). Acta Cryst. F67, 730-733.