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Chapter 2 : Crystal Structure of the Large Ribosomal Subunit at 5-Angstrom Resolution

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Crystal Structure of the Large Ribosomal Subunit at 5-Angstrom Resolution, Page 1 of 2

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Abstract:

The ribonucleoproteins called ribosomes were discovered by cytologists in the mid-1950s, and by 1960 it was apparent that they catalyze protein synthesis. Ribosomes consume aminoacyl transfer RNAs, and the sequences of the proteins they produce are determined by those of the mRNAs with which they interact. The first ribosome crystals did not diffract to atomic resolution, but even if they had, it is uncertain what would have come of it in the short term; their analysis would have severely tested the crystallographic technology of the day. Heavy-atom cluster compounds are useful for phasing macromolecular diffraction patterns of large macromolecules at low resolution. The structure of an ordinary macromolecular crystal is solved when the experimental phases available are accurate to a resolution high enough so that an all-atom model of the molecule’s sequence can be fitted into the resulting electron density map. ESSENS can also be used to find less generic structures, such as the sarcin-ricin loop (SRL). The SRL is a critical part of the factor binding center, or GTPase center, of the large ribosomal subunit. A conformational change that moves L11 and its associated rRNA towards the putative factor binding site seems at least equally likely, and since there is no ribosomal material in the way to prevent it, that kind of motion is possible. In this connection, it is interesting to note that there is a substantial literature indicating that this part of the ribosome does indeed move during protein synthesis.

Citation: Ban N, Nissen P, Moore P, Steitz T. 2000. Crystal Structure of the Large Ribosomal Subunit at 5-Angstrom Resolution, p 11-20. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch2

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Figures

Image of Figure 1
Figure 1

Four versions of the electron density in a specific region of the large ribosomal subunit from . (A) The region as it appeared in the 9-Å-resolution map published in 1998 ( ) with an approximate molecular interpretation supplied. (B) The same region in a map computed with the phases available today, also to 9-Å resolution. (C) The region at the full resolution available today (5Å ). (D) The electron density expected if the atomic structure shown were the correct structure and if the resolution limit was in fact 5 Å . Panel D was computed by assuming a temperature factor of 80 Å, which is appropriate for the crystals under investigation. Molecular models were prepared with the O program, and the illustrations were prepared with both O and RIBBONS ( ).

Citation: Ban N, Nissen P, Moore P, Steitz T. 2000. Crystal Structure of the Large Ribosomal Subunit at 5-Angstrom Resolution, p 11-20. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch2
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Image of Figure 2
Figure 2

A surface rendering of the large ribosomal subunit in the crown view. (Top) Stereo view of the subunit with EFG docked to the factor binding center. EF-G is the protein whose ribbon diagram is colored purple. (Bottom) The same view of the subunit with EF-G removed so that the factor binding center can be seen. In both panels, segments of helical RNA (white backbone) are inserted into the density in several places to guide the reader. Also inserted are ribbon diagrams for proteins L2, L6, L11, and L14 (yellow), the SRL (red backbone), two other segments of domain IV (blue backbone), and the thiostrepton binding segment of 23S rRNA (orange backbone). The position where L1 is seen in lower-resolution maps (see the text) is also indicated.

Citation: Ban N, Nissen P, Moore P, Steitz T. 2000. Crystal Structure of the Large Ribosomal Subunit at 5-Angstrom Resolution, p 11-20. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch2
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Image of Figure 3
Figure 3

Electron density in the L2 region. Electron density corresponding to the RNA binding domain of L2 is shown adjacent to the stem-loop that forms the bottom of the L1 stalk. It is clear that RNA can easily be distinguished from protein in these maps. (It should be noted that the atomic structures shown in this and all other figures have been fitted into the electron density by hand. No effort has been made to optimize these fits computationally. Furthermore, in every case, the protein structures used are those of homologues of the proteins in question, not the structures of the proteins themselves, none of which are known. Since the sequences of these homologues are not the same as those of the proteins they are being used to represent, some divergence between the structures used and the electron density into which they are fitted is to be expected.)

Citation: Ban N, Nissen P, Moore P, Steitz T. 2000. Crystal Structure of the Large Ribosomal Subunit at 5-Angstrom Resolution, p 11-20. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch2
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Image of Figure 4
Figure 4

L6 and the rRNA segments with which it interacts. The backbone structure of L6 is shown superimposed on the electron density assigned to it. Four rRNA segments interact with L6, and the SRL is on the far right.

Citation: Ban N, Nissen P, Moore P, Steitz T. 2000. Crystal Structure of the Large Ribosomal Subunit at 5-Angstrom Resolution, p 11-20. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch2
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Image of Figure 5
Figure 5

Stereo views of a model for the interaction of EF-G and the EF-Tu•tRNA complex with the factor binding center of the large ribosomal subunit. (Top) A view of the model in the same orientation as in Fig. 2 , top. EF-G is shown in purple, the SRL is red, a helix is blue, helix 97 is yellow, and the thiostrepton RNA is orange. All ribosomal proteins are gray. (Middle) The same model as in the top panel, viewed from the top with the L11-rRNA assembly removed so that the interaction proposed to occur between the SRL and EF-G can be visualized. (Bottom) The same view as the middle panel with EF-G replaced by the EF-Tu•tRNA complex. The tRNA backbone is magenta.

Citation: Ban N, Nissen P, Moore P, Steitz T. 2000. Crystal Structure of the Large Ribosomal Subunit at 5-Angstrom Resolution, p 11-20. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch2
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References

/content/book/10.1128/9781555818142.chap2
1. Abrahams, J. P.,, and A. G. W. Leslie. 1996. Methods used in the structure determination of bovine mitochondrial F1 ATPase. Acta Crystallogr. D52:3042.
2. Agrawal, R. K.,, P. Penczek,, R. A. Grassucci,, and J. Frank. 1998. Visualization of elongation factor G on the Escherichia coli 70S ribosome: the mechanism of translocation. Proc. Natl. Acad. Sci. USA 95:61346138.
3. Agrawal, R. K.,, R. K. Lata,, and J. Frank. 1999. Conformational variability in Escherichia coli 70S ribosome as revealed by 3D cryo-electron microscopy. Int. J. Biochem. Cell Biol. 31:243254.
4. Ban, N.,, B. Freeborn,, P. Nissen,, P. Penczek,, R. A. Grassucci,, R. Sweet,, J. Frank,, P. B. Moore,, and T. A. Steitz. 1998. A 9 A resolution X-ray crystallographic map of the large ribosomal subunit. Cell 93:11051115.
5. Ban, N.,, P. Nissen,, J. Hansen,, M. Capel,, P. B. Moore,, and T. A. Steitz. 1999. Placement of protein and RNA structures into a 5 Å-resolution map of the 50S ribosomal subunit. Nature 400: 841847.
6. Byers, B. 1966. Ribosome crystallization induced in chick embryo tissue by hypothermia. J. Cell Biol. 30:C1.
7. Carson, M. 1991. Ribbons 2.0. J. Appl. Crystallogr. 24:103106.
8. Clark, M. W.,, M. Hammons,, J. A. Langer,, and J. A. Lake. 1979. Helical arrays of Escherichia coli small ribosomal subunits produced in vitro. J. Mol. Biol. 135:507512.
9. Clark, M. W.,, K. Leonard,, and J. A. Lake. 1982. Ribosomal crystalline arrays of large subunits from E. coli. Science 216:999.
10. Conn, G. L.,, D. E. Draper,, E. E. Lattman,, and A. G. Gittis. 1999. Crystal structure of a conserved ribosomal protein RNA complex. Science 284:11711174.
11. Correll, C. C.,, A. Munishkin,, Y. Chan,, Z. Ren,, I. G. Wool,, and T. A. Steitz. 1998. Crystal structure of the ribosomal RNA loop essential for binding both elongation factors. Proc. Natl. Acad. Sci. USA 95:1343613441.
12. Cowtan, K. D. 1994. An automated procedure for phase improvement by density modification. Jt. CCP4 ESF-EACBM Newsl. Protein Crystallogr. 31:3438.
13. Davies, C.,, S. W. White,, and V. Ramakrishnan. 1996. The crystal structure of ribosomal protein L14 reveals an important organizational component of the translational apparatus. Structure 4: 5566.
14. Frank, J. 1999. The ribosome—structure and functional ligand-binding experiments using cryo-electron microscopy. J. Struct. Biol. 124:142150.
15. Frank, J.,, A. Verschoor,, Y. Li,, J. Zhu,, R. K. Lata,, M. Rademacher,, P. Penczek,, R. Grassucci,, R. K. Agrawal,, and S. Srivastava. 1995. A model of the translational apparatus based on a three-dimensional reconstruction of the Escherichia coli ribosome. Biochem. Cell Biol. 73:757765.
16. Golden, B. L.,, V. Ramakrishnan,, and S. W. White. 1993. Ribosomal protein L6. Structural evidence of gene duplication from a primitive RNA binding protein. EMBO J. 12:49014908.
17. Gutell, R. R.,, M. W. Gray,, and M. N. Schnare. 1993. A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993. Nucleic Acids Res. 21:30553074.
18. Hope, H.,, F. Frolow,, K. von Bohlen,, I. Makowski,, C. Kratky,, Y. Halfori,, H. Danz,, P. Webster,, K. S. Bartles,, H. G. Wittmann,, and A. Yonath. 1989. Cryocrystallography of ribosomal particles. Acta Crystallogr. B45:190199.
19. Jack, A.,, S. C. Harrison,, and R. A. Crowther. 1975. Structure of tomato bushy stunt virus. II. Comparison of results obtained by electron microscopy and X-ray diffraction. J. Mol. Biol. 97:163172.
20. Jones, T. A., 1992. A set of averaging programs, p. 91105. In E. J. Dodson,, S. Glover,, and W. Wolf (ed.), CCP4 Study Weekend, Molecular Replacement. Daresbury Laboratory, Warrington, United Kingdom.
21. Jones, T. A.,, S. Cowan,, J.-Y. Zou,, and M. Kjeldgaard. 1991. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A46:110119.
22. Kleywegt, G. J.,, and T. A. Jones. 1997. Template convolution to enhance or detect structural features in macromolecular electron-density maps. Acta Crystallogr. D53:179185.
23. Ladenstein, R.,, A. Bacher,, and R. Huber. 1987. Some observations of a correlation between the symmetry of large heavy-atom compounds and their binding sites on proteins. J. Mol. Biol. 195: 751753.
24. Leffers, H.,, J. Kjems,, L. Ostergaard,, N. Larsen,, and R. A. Garrett. 1987. Evolutionary relationships amongst archaebacteria: a comparative study of 23S ribosomal RNAs of a sulphur-dependent extreme thermophile, an extreme halophile, and a thermophilic methanogen. J. Mol. Biol. 195:4361.
25. Leffers, H.,, J. Egeberg,, A. Andersen,, T. Christensen,, and R. A. Garrett. 1988. Domain VI of Escherichia coli 23 S ribosomal RNA. Structure, assembly and function. J. Mol. Biol. 204:507522.
26. Liljas, A.,, L. A. Kirsebom,, and M. Leijonmarck,. 1986. Structural studies of the factor binding domain, p. 379390. In B. Hardesty, and G. Kramer (ed.), Structure, Function and Genetics of Ribosomes. Springer-Verlag, New York, N.Y.
27. Macbeth, M. R.,, and I. G. Wool. 1999. The phenotype of mutations of G2655 in the sarcin / ricin domain of 23S ribosomal RNA. J. Mol. Biol. 285:965975.
28. Moazed, D.,, J. M. Roberston,, and H. F. Noller. 1988. Interaction of elongation factors EF-G and EF-Tu with a conserved loop in 23S RNA. Nature 334:362364.
29. Moller, W.,, P. I. Schrier,, J. A. Maassen,, A. Zanteva,, E. Schop,, and H. Reinalda. 1983. Ribosomal proteins L7/L12 of E. coli. Localization and possible molecular mechanism in translation. J. Mol. Biol. 163:553573.
30. Munishkin, A.,, and I. G. Wool. 1997. The ribosome-in-pieces: binding of elongation factor EF-G to oligoribonucleotides that mimic the sarcin / ricin and thiostrepton domains of 23S ribosomal RNA. Proc. Natl. Acad. Sci. USA 94:1228012284.
31. Nakagawa, A.,, T. Nakashima,, M. Taniguchi,, H. Hosaka,, M. Kimura,, and I. Tanaka. 1999. The three-dimensional structure of the RNA-binding domain of ribosomal protein L2; a protein at the peptidyl transferase center of the ribosome. EMBO J. 18: 14591467.
32. Nissen, P.,, M. Kjeldgaard,, S. Thirup,, G. Polekhina,, L. Reshetnikova,, B. F. Clark,, and J. Nyborg. 1995. Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. Science 270:14641472.
33. Oakes, M. I.,, A. Scheinman,, T. Atha,, G. Shankweiler,, and J. A. Lake,. 1990. Ribosome structure: three-dimensional locations of rRNA and proteins, p. 180193. In W. E. Hill,, A. E. Dahlberg,, R. A. Garrett,, P. B. Moore,, D. Schlessinger,, and J. R. Warner (ed.), The Ribosome. Structure, Function, and Evolution. American Society for Microbiology, Washington, D.C.
34. O’Halloran, T. V.,, S. J. Lippard,, T. J. Richmond,, and A. Klug. 1987. Multiple heavy-atom reagents for macromolecular X-ray structure determination. Application to the nucleosome core particle. J. Mol. Biol. 194:705712.
35. Porse, B. T.,, E. Cundliffe,, and R. A. Garrett. 1999. The antibiotic micrococcin acts on protein L11 at the ribosomal GTPase centre. J. Mol. Biol. 287:3345
36. Schlunzen, F.,, H. A. S. Hansen,, J. Thygesen,, W. S. Bennett,, N. Volkmann,, I. Levin,, J. Harms,, H. Bartles,, A. Zaytzev-Bashan,, Z. Berkovitch-Yellin,, I. Sagi,, F. Fransceschi,, S. Krumbholtz,, M. Geva,, S. Weinstein,, I. Agmon,, N. Boddeker,, S. Morlang,, R. Sharon,, A. Dribin,, E. Maltz,, M. Peretz,, V. Weinrich,, and A. Yonath. 1995. A milestone in ribosomal crystallography: the construction of preliminary electron density maps at intermediate resolution. Biochem. Cell Biol. 73:739749.
37. Shoham, M.,, H. G. Wittmann,, and A. Yonath. 1987. Single crystals of large ribosomal particles from Halobacterium marismortui diffract to 6 A. J. Mol. Biol. 193:819822.
38. Stark, H.,, M. V. Rodnin,, J. Rinke-Appel,, R. Brimacombe,, W. Wintermeyer,, and M. van Heel. 1997. Visualization of elongation factor Tu on the Escherichia coli ribosome. Nature 389:403406.
39. Stoeffler-Meilicke, M.,, and G. Stoeffler,. 1990. Topography of the ribosomal proteins from Escherichia coli within the intact subunits as determined by immunoelectron microscopy and protein-protein cross-linking, p. 123133. In W. E. Hill,, A. Dahlberg,, R. A. Garrett,, P. B. Moore,, D. Schlessinger,, and J. R. Warner (ed.), The Ribosome. Structure, Function, and Evolution. American Society for Microbiology, Washington, D.C.
40. Szewczak, A. A.,, and P. B. Moore. 1995. The sarcin / ricin loop, a modular RNA. J. Mol. Biol. 247:8198.
41. Thompson, J.,, and E. Cundliffe. 1991. The binding of thiostrepton to 23S ribosomal RNA. Biochimie 73:11311135.
42. Tissieres, A., 1974. Ribosome research: historical background, p. 312. In M. Nomura,, A. Tissieres,, and P. Lengyel (ed.), Ribosomes. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
43. Traut, R. R.,, D. S. Tewari,, A. Sommer,, G. R. Gavino,, H. M. Olson,, and D. G. Glitz,. 1986. Protein topography of ribosomal functional domains: effects of monoclonal antibodies to different epitopes in Escherichia coli protein L7/L12 on ribosome function and structure, p. 286308. In B. Hardesty, and G. Kramer, (ed.), Structure, Function, and Genetics of Ribosomes. Springer-Verlag, New York, N.Y.
44. Uchiumi, T.,, N. Sato,, A. Wada,, and A. Hachimori. 1999. Interaction of the sarcin / ricin domain of 23S ribosomal RNA with proteins L3 and L6. J. Biol. Chem. 274:681686.
45. von Bohlen, K.,, I. Makowski,, H. A. S. Hansen,, H. Bartels,, Z. Berkovitch-Yellin,, A. Zaytzev-Bushan,, S. Meyer,, C. Paulke,, F. Franceschi,, and A. Yonath. 1991. Characterization and preliminary attempts for derivatization of crystals of large ribosomal subunits from Haloarcula marismortui diffracting to 3 A resolution. J. Mol. Biol. 222:1115.
46. Wilson, K. S.,, and H. F. Noller. 1998. Mapping the position of translational elongation factor EF-G in the ribosome by directed hydroxyl radical probing. Cell 92:131139.
47. Wimberly, B. T.,, R. Guymon,, J. P. McCutcheon,, S. W. White,, and V. R. Ramakrishnan. 1999. A detailed view of a ribosomal active site: the structure of the L11-RNA complex. Cell 97:491502.
48. Wool, I. G.,, A. Gluck,, and Y. Endo. 1992. Ribotoxin recognition of ribosomal RNA and a proposal for the mechanism of translocation. Trends Biochem. Sci. 17:266269.
49. Yonath, A.,, J. Mussig,, B. Tesche,, S. Lorenz,, V. A. Erdmann,, and H. G. Wittmann. 1980. Crystallization of the large ribosomal subunits from Bacillus stearothermophilus. Biochem. Int. 1:428435.
50. Yonath, A.,, J. Harms,, H. A. S. Hansen,, A. Bashan,, F. Schlunzen,, I. Levin,, I. Koelln,, A. Tocili,, I. Agmon,, M. Peretz,, H. Bartles,, W. S. Bennett,, S. Krumbholz,, D. Janell,, S. Weinstein,, T. Auerbach,, H. Avila,, M. Pioletti,, S. Morlang,, and F. Franceschi. 1998. Crystallographic studies on the ribosome, a large macromolecular assembly exhibiting severe non-isomorphism, extreme beam sensitivity and no internal symmetry. Acta Crystallogr. A54:945955.

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