Crystallization of RNA-protein complexes

Methods in Molecular Biology

Volumn 363, Issue , 2007, Pages 259-276

  Obayashi, Eiji ^a   Oubridge, Chris ^a   Krummel, Daniel Pomeranz ^a   Nagai, Kiyoshi ^a  

^a NONE

Author keywords

Crystals; RNA binding proteins; RNA protein complex

Indexed keywords

RIBONUCLEOPROTEIN; RNA; RNA BINDING PROTEIN;

ARTICLE; BINDING SITE; CHEMISTRY; CRYSTALLIZATION; METHODOLOGY; PROTEIN DATABASE;

BINDING SITES; CRYSTALLIZATION; DATABASES, PROTEIN; RIBONUCLEOPROTEINS; RNA; RNA-BINDING PROTEINS;

EID: 33847268784     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1385/1-59745-209-2:259     Document Type: Article

References (72)

1. Cech, T. R. and Bass, B. L. (1986) Biological catalysis by RNA. Annu. Rev. Biochem. 55, 599-629.
2. Watson, J. D., Hopkins, N. H., Roberts, J. W., Steitz, J. A., and Weiner, A. M. (1987) Molecular Biology of the Gene, 4th ed. The Benjamin/Cummings Publishing Company, Inc., Menlo Park, CA.
3. Gopalan, V., Talbot, S. J., and Altman, S. (1994) RNA-protein interactions in RNase P, in RNA-Protein Interactions, (Nagai, K. and Mattaj, I. W., eds.), Oxford University Press, New York, pp. 103-126.
4. McCloskey, J. A. and Crain, P. (1998) The RNA modification database-1998. Nucleic Acids Res. 26, 192-197.
5. Li, F., Xiong, Y., Wang, J., et al. (2002) Crystal structures of the Bacillus stearothermophilus CCA-adding enzyme and its complexes with ATP or CTP. Cell 111, 816-824.
6. Cusack, S. (1997) Aminoacyl-tRNA synthetases. Curr. Opin. Struct. Biol. 7, 881-889.
7. Nissen, P., Kjeldgaard, M., Thirup, S., et al. (1995) Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. Science 270, 1464-1472.
8. Ramakrishnan, V. (2002) Ribosome structure and the mechanism of translation. Cell 108, 557-572.
9. Bürge, C. B., Tuschl, T., and Sharp, P. A. (1999) Splicing of Precursors to mRNA by the spliceosome, in The RNA World 2nd ed., (Gesteland, R. F., Cech, T. R., and Atkins, J. F., eds.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 525-560.
10. Yu, Y. -T., Scharl, E. C., Smith, C. M., and Steitz, J. A. (1999) The growing world of small nuclear ribonucleoproteins, in The RNA World, 2nd ed., (Gesteland, R. F., Cech, T. R., and Atkins, J. F., eds.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 487-524.
11. Nagai, K., Oubridge, C., Kuglstatter, A., Menichelli, E., Isel, C., and Jovine, L. (2003) Structure, function and evolution of the signal recognition particle. EMBO J. 22, 3479-3485.
12. Blackburn, E. H. (1999) Telomerases, in The RNA World, 2nd ed., (Gesteland, R. F., Cech, T. R., and Atkins, J. F., eds.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 609-635.
13. Rould, M. A., Perona, J. J., Söll, D., and Steitz, T. A. (1989) Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 Å resolution. Science 246, 1135-1142.
14. Ruff, M., Krishnaswamy, S., Boeglin, M., et al. (1991) Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). Science 252, 1682-1689.
15. Biou, V., Yaremchuk, A., Tukalo, M., and Cusack, S. (1994) The 2.9 Åcrystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser). Science 263, 1404-1410.
16. Valegård, K., Murray, J. B., Stockley, P. G., Stonehouse, N. J., and Liljas, L. (1994) Crystal structure of an RNA bacteriophage coat protein-operator complex. Nature 371, 623-626.
17. Oubridge, C., Ito, N., Evans, P. R., Teo, C. H., and Nagai, K. (1994) Crystal structure at 1.92 Åresolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature 372, 432-438.
18. Oubridge, C., Ito, N., Teo, C. H., Fearnley, I., and Nagai, K. (1995) Crystallisation of RNA-protein complexes. II. The application of protein engineering for crystallisation of the U1A protein-RNA complex. J. Mol. Biol. 249, 409-423.
19. Jaeger, J. A., Turner, D. H., and Zuker, M. (1990) Predicting optimal and suboptimal secondary structure for RNA. Methods Enzymol. 183, 281-306.
20. Westhof, E. and Michel, F. (1994) Prediction and experimental investigation of RNA secondary and tertiary foldings. In: RNA-Protein Interactions, (Nagai, K. and Mattaj, I. W., eds.), Oxford University Press, New York, pp. 25-51.
21. Brunel, C. and Romby, P. (2000) Probing RNA structure and RNA-ligand complexes with chemical probes. Methods Enzymol. 318, 3-21.
22. Merryman, C. and Noller, H. F. (1998) Footprinting and modification-interference analysis of binding sites on RNA. In: RNA:Protein Interactions; A Practical Approach, (Smith, C. W. J., ed.), Oxford University Press, New York, pp. 237-253.
23. Price, S. R., Evans, P. R., and Nagai, K. (1998) Crystal structure of the spliceosomal U2B"-U2A protein complex bound to a fragment of U2 small nuclear RNA. Nature 394, 645-650.
24. Wu, X. and Pitsch, S. (1998) Synthesis and pairing properties of oligoribonucleotide analogues containing a metal-binding site attached to β-D-allofuranosyl cytosine. Nucleic Acids Res. 26, 4315-4323.
25. Scaringe, S. A., Wincott, F. E., and Caruthers, M. H. (1998) Novel RNA synthesis method using 5′-O-silyl-2′-O-orthoester protecting groups. J. Am. Chem. Soc. 120, 11,820-11,821.
26. Davanloo, P., Rosenberg, A. H., Dunn, J. J., and Studier, F. W. (1984) Cloning and expression of the gene for bacteriophage T7 RNA polymerase. Proc. Natl. Acad. Sci. USA 81, 2035-2039.
27. Cheetham, G. M. and Steitz, T. A. (1999) Structure of a transcribing T7 RNA polymerase initiation complex. Science 286, 2305-2309.
28. Yin, Y. W. and Steitz, T. A. (2002) Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase. Science 298, 1387-1395.
29. Tahirov, T. H., Temiakov, D., Anikin, M., et al. (2002) Structure of a T7 RNA polymerase elongation complex at 2.9 Å resolution. Nature 420, 43-50.
30. Milligan, J. F., Groebe, D. R., Witherell, G. W., and Uhlenbeck, O. C. (1987) Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucl. Acids Res. 15, 8783-8798.
31. Milligan, J. F. and Uhlenbeck, O. C. (1989) Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol. 180, 51-62.
32. Price, S. R., Oubridge, C., Varani, G., and Nagai, K. (1998) Preparation of RNA: protein complexes for x-ray crystallography and NMR. In: RNA:Protein Interactions; A Practical Approach, (Smith, C. W. J., ed.), Oxford University Press, New York, pp. 37-74.
33. Schenborn, E. T. and Mierendorf, R. C., Jr. (1985) A novel transcription property of SP6 and T7 RNA polymerases: dependence on template structure. Nucl. Acids Res. 13, 6223-6236.
34. Price, S. R., Ito, N., Oubridge, C., Avis, J. M., and Nagai, K. (1995) Crystallisation of RNA-protein complexes. I. Methods for the large-scale preparation of RNA suitable for crystallographic studies. J. Mol. Biol. 249, 398-408.
35. Pleiss, J. A., Derrick, M. L., and Uhlenbeck, O. C. (1998) T7 RNA polymerase produces 5' end heterogeneity during in vitro transcription from certain templates. RNA 4, 1313-1317.
36. Helm, M., Brule, H., Giege, R., and Florentz, C. (1999) More mistakes by T7 RNA polymerase at the 5' ends of in vitro-transcribed RNAs. RNA 5, 618-621.
37. Sheldon, C. C. and Symons, R. H. (1989) Mutagenesis analysis of a self-cleaving RNA. Nucl. Acids Res. 17, 5679-5685.
38. Perriman, R., Delves, A., and Gerlach, W. L. (1992) Extended target site specificity for a hammerhead ribozyme. Gene 113, 157-163.
39. Koizumi, M., Hayase, Y., Iwai, S., Kamiya, H., Inoue, H., and Ohtsuka, E. (1989) Design of RNA enzymes distinguishing a single base mutation in RNA. Nucl. Acids Res. 17, 7059-7071.
40. Ferré-D' Amaré, A. R., Zhou, K., and Doudna, J. A. (1998) Crystal structure of a hepatitis delta virus ribozyme. Nature 395, 567-574.
41. Searles, M. A., Lu, D., and Klug, A. (2000) The role of the central zinc fingers of transcription factor IIIA in binding to 5S RNA. J. Mol. Biol. 301, 47-60.
42. Scherly, D., Boelens, W., Dathan, N. A., van Venrooij, W. J., and Mattaj, I. W. (1990) Major determinants of the specificity of interaction between small nuclear ribonucleoproteins U1A and U2B" and their cognate RNAs. Nature 345, 502-506.
43. Cline, T. W. and Meyer, B. J. (1996) Vive la difference: males vs females in flies vs worms. Annu. Rev. Genet. 30, 637-702.
44. Adam, S. A., Nakagawa, T., Swanson, M. S., Woodruff, T. K., and Dreyfuss, G. (1986) mRNA polyadenylate-binding protein: gene isolation and sequencing and identification of a ribonucleoprotein consensus sequence. Mol. Cell Biol. 6, 2932-2943.
45. Miller, J., McLachlan, A. D., and Klug, A. (1985) Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J. 4, 1609-1614.
46. Jessen, T. H., Oubridge, C., Teo, C. H., Pritchard, C., and Nagai, K. (1991) Identification of molecular contacts between the U1A small nuclear ribonucleoprotein and U1 RNA. EMBO J. 10, 3447-3456.
47. Sachs, A. B., Bond, M. W., and Kornberg, R. D. (1986) A single gene from yeast for both nuclear and cytoplasmic polyadenylate-binding proteins: domain structure and expression. Cell 45, 827-835.
48. Scherly, D., Boelens, W., van Venrooij, W. J., Dathan, N. A., Hamm, J., and Mattaj, I. W. (1989) Identification of the RNA binding segment of human U1A protein and definition of its binding site on U1 snRNA. EMBO J. 8, 4163-4170.
49. Theunissen, O., Rudt, F., Guddat, U., Mentzel, H., and Pieler, T. (1992) RNA and DNA binding zinc fingers in Xenopus TFIIIA. Cell 71, 679-690.
50. Cohen, S. L., Ferré-D' Amaré, A. R., Burley, S. K., and Chait, B. T. (1995) Probing the solution structure of the DNA-binding protein Max by a combination of proteolysis and mass spectrometry. Protein Sci. 4, 1088-1099.
51. Oubridge, C., Kuglstatter, A., Jovine, L., and Nagai, K. (2002) Crystal structure of SRP19 in complex with the S domain of SRP RNA and its implication for the assembly of the signal recognition particle. Mol. Cell 9, 1251-1261.
52. Kuglstatter, A., Oubridge, C., and Nagai, K. (2002) Induced structural changes of 7SL RNA during the assembly of human signal recognition particle. Nat. Struct. Biol. 9, 740-744.
53. Golden, B. L. and Kundrot, C. E. (2003) RNA crystallisation. J. Struct. Biol. 141, 98-107.
54. Jovine, L., Hainzl, T., Oubridge, C., and Nagai, K. (2000) Crystallisation and preliminary X-ray analysis of the conserved domain IV of Escherichia coli 4.5S RNA. Acta Crystallogr. D Biol. Crystallogr. 56, 1512.
55. Jovine, L., Hainzl, T., Oubridge, C., et al. (2000) Crystal structure of the ffh and EF-G binding sites in the conserved domain IV of Escherichia coli 4.5S RNA. Structure Fold. Des. 8, 527-540.
56. Holbrook, S. R., Cheong, C., Tinoco, I. Jr., and Kim, S. H. (1991) Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base pairs. Nature 353, 579-581.
57. Ennifar, E., Walter, P., Ehresmann, B., Ehresmann, C., and Dumas, P. (2001) Crystal structures of coaxially stacked kissing complexes of the HIV-1 RNA dimerization initiation site. Nat. Struct. Biol. 8, 1064-1068.
58. Muto, Y., Pomeranz Krummel, D., Oubridge, C., et al. (2005) The structure and biochemical properties of the human spliceosomal protein U1C. J. Mol. Biol. 341, 185-198.
59. Nomura, M., Traub, P., and Bechmann, H. (1968) Hybrid 30S ribosomal particles reconstituted from components of different bacterial origins. Nature 219, 793-799.
60. Will, C. L. and Lührmann, R. (2001) Spliceosomal UsnRNP biogenesis, structure and function. Curr. Opin. Cell Biol. 13, 290-301.
61. Pellizzoni, L., Yong, J., and Dreyfuss, G. (2002) Essential role for the SMN complex in the specificity of snRNP assembly. Science 298, 1775-1779.
62. Mattaj, I. W. (1986) Cap trimethylation of U snRNA is cytoplasmic and dependent on U snRNP protein binding. Cell 46, 905-911.
63. Hetzer, M. and Mattaj, I. W. (2000) An ATP-dependent, Ran-independent mechanism for nuclear import of the U1A and U2B′ spliceosome proteins. J. Cell. Biol. 148, 293-303.
64. Sobott, F. and Robinson, C. V. (2002) Protein complexes gain momentum. Curr. Opin. Struct. Biol. 12, 729-734.
65. Golden, B. L. and Kundrot, C. E. (2003) RNA crystallisation. J. Struct. Biol. 141, 98-107.
66. Aggarwal, A. K. (1990) Crystallisation of DNA binding proteins with oligodeoxynucleotides. Methods 1, 83-90.
67. Perona, J. J. (1990) Crystallisation of RNA-protein complexes. Methods 1, 75-82.
68. Schmitt, E., Panvert, M., Blanquet, S., and Mechulam, Y. (1998) Crystal structure of methionyl-tRNAfMet transformylase complexed with the initiator formylmethionyl-tRNAfMet. EMBO J. 17, 6819-6826.
69. Batey, R. T., Rambo, R. P., Lucast, L., Rha, B., and Doudna, J. A. (2000) Crystal structure of the ribonucleoprotein core of the signal recognition particle. Science 287, 1232-1239.
70. Sauter, C., Ng, J. D., Lorber, B., et al. (1999) Additives for the crystallisation of proteins and nucleic acids. J. Cryst. Growth 196, 365-376.
71. Ryter, J. M. and Schultz, S. C. (1998) Molecular basis of double-stranded RNA-protein interactions: structure of a dsRNA-binding domain complexed with dsRNA. EMBO J. 17, 7505-7513.
72. Antson, A. A., Dodson, E. J., Dodson, G., Greaves, R. B., Chen, X., and Gollnick, P. (1999) Structure of the trp RNA-binding attenuation protein, TRAP, bound to RNA. Nature 401, 235-242.