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Chapter 3 : Identification of Selected Ribosomal Components in Crystallographic Maps of Prokaryotic Ribosomal Subunits at Medium Resolution

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Identification of Selected Ribosomal Components in Crystallographic Maps of Prokaryotic Ribosomal Subunits at Medium Resolution, Page 1 of 2

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Abstract:

This chapter focuses on the electron density map of the small ribosomal subunit, shows features interpreted as ribosomal proteins and rRNA, and pinpoints secondary-structure elements. It highlights the use of heavy-atom markers for unbiased targeting of surface rRNA (e.g., the 3 end of the 16S RNA) and for the localization of proteins TS11 and TS13. Efforts to induce controlled conformational changes within the crystals are also discussed in the chapter. The globular regions of lower density could be assigned to folds observed in isolated ribosomal proteins as determined by nuclear magnetic resonance (NMR) and crystallography at atomic resolution. The globular regions seen in the maps, most of which are of lower average density, were found appropriate to accommodate ribosomal proteins. The main chain coordinates, as determined by X-ray crystallography or NMR for the isolated proteins at high resolution, were used as templates. The chapter talks about structural markers targeted to predetermined sites, and functional activation in pre-and postcrystallization states. Despite severe crystallographic problems, the way to structure determination has been paved and electron density maps at close to molecular resolution are emerging. The growing popularity of ribosomal crystallography is indeed gratifying. This, together with the fruitful interactions with the exciting advances in cryo-EM, is bound to lead to major breakthroughs.

Citation: Bashan A, Bartels H, Levin I, Peretz M, Agmon I, Kessler M, Weinstein S, Pioletti M, Avila H, Simitsopoulou M, Franceschi F, Janell D, Schluenzen F, Gluehmann M, Harms J, Hansen H, Tocilji A, Bennett W, Auerbach T, Yonath A. 2000. Identification of Selected Ribosomal Components in Crystallographic Maps of Prokaryotic Ribosomal Subunits at Medium Resolution, p 21-33. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch3

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Figures

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Figure 1

(a) The 7.2-Å map of T30S, contoured at 1.3 σ and sectioned in a direction allowing comparison to the available EM reconstructions of the T70S-bound T30S particle ( ) (b) and the E30S conformer resembling that seen in 70S ribosomes to which fMet-tRNA is bound ( ) (c). A total of 21,000 unique reflections at the range 7.2 to 12.5 Å were included. Four derivatives were used: mercury acetate, platinum tetrachloride, TaBr, and CHgNO. The final statistics were as follows: FOM = 0.671; phasing power = 1.4, = 0.8 to 0.91. For the 5-Å map, phase information was added from an additional heavy-atom derivative, methyl-mercury acetate, that was bound to the particle prior to crystallization. A total of 62,037 reflections were used. The final FOM was 0.77, and the phasing power was 1.25. bk, beak; ch, channel; sp, spur; sf, shoulder finger; pf, platform finger; s, shoulder; h, head; p, platform.

Citation: Bashan A, Bartels H, Levin I, Peretz M, Agmon I, Kessler M, Weinstein S, Pioletti M, Avila H, Simitsopoulou M, Franceschi F, Janell D, Schluenzen F, Gluehmann M, Harms J, Hansen H, Tocilji A, Bennett W, Auerbach T, Yonath A. 2000. Identification of Selected Ribosomal Components in Crystallographic Maps of Prokaryotic Ribosomal Subunits at Medium Resolution, p 21-33. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch3
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Image of Figure 2
Figure 2

RNA chains fitted into the 7.2-Å map of T30S (contour levels, 1.25 σ). Except for those shown in the lower right two panels, all of the chains were fitted manually, using building blocks of the canonical A-form RNA duplex (mainly 5 by 2 bases). The two views shown at the lower right were located semi-automatically, using as building blocks the CCA end of the tRNA molecule ( ). The large sphere shown in the center right panel between two helical regions represents a heavy-atom cluster.

Citation: Bashan A, Bartels H, Levin I, Peretz M, Agmon I, Kessler M, Weinstein S, Pioletti M, Avila H, Simitsopoulou M, Franceschi F, Janell D, Schluenzen F, Gluehmann M, Harms J, Hansen H, Tocilji A, Bennett W, Auerbach T, Yonath A. 2000. Identification of Selected Ribosomal Components in Crystallographic Maps of Prokaryotic Ribosomal Subunits at Medium Resolution, p 21-33. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch3
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Image of Figure 3
Figure 3

The main chain of the RNA binding domain of the X-ray-determined structure of protein TS5 (shown in yellow-green) overlaid on the 7.2-Å map (contoured at a signal-to-noise ratio of 0.8 [dark green] and at 1.3 σ [blue]). Note that a fair portion of the protein surface is in contact with other prominent features.

Citation: Bashan A, Bartels H, Levin I, Peretz M, Agmon I, Kessler M, Weinstein S, Pioletti M, Avila H, Simitsopoulou M, Franceschi F, Janell D, Schluenzen F, Gluehmann M, Harms J, Hansen H, Tocilji A, Bennett W, Auerbach T, Yonath A. 2000. Identification of Selected Ribosomal Components in Crystallographic Maps of Prokaryotic Ribosomal Subunits at Medium Resolution, p 21-33. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch3
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Figure 4

(a to d) About two-thirds of the backbone of protein TS7 fitted into the 7.2-Å map. The remaining third has been removed for clarity. Each dark-yellow sphere represents an amino acid. All atoms of the RNA chains are shown. (a and b) Space-filling presentation of TS7 surrounded by several features, among which one was fitted as an RNA duplex of 2 by 6 bases (shown as sticks in panel a and as a space-filling model in panel b. (c and d) Representations similar to that in panel b, but half a duplex has been removed, and a slice of it is shown, highlighting the contacts between the proteins and the RNA and the space available for the protein side chains (not shown). (e) The quality of the fitting is shown by a ribbon representing the main chain.

Citation: Bashan A, Bartels H, Levin I, Peretz M, Agmon I, Kessler M, Weinstein S, Pioletti M, Avila H, Simitsopoulou M, Franceschi F, Janell D, Schluenzen F, Gluehmann M, Harms J, Hansen H, Tocilji A, Bennett W, Auerbach T, Yonath A. 2000. Identification of Selected Ribosomal Components in Crystallographic Maps of Prokaryotic Ribosomal Subunits at Medium Resolution, p 21-33. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch3
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Image of Figure 5
Figure 5

The suggested locations of the 3' end of the 16S RNA (yellow-green) as detected by the Fourier method overlaid on the part of the 7.2-Å map assigned to T30S.

Citation: Bashan A, Bartels H, Levin I, Peretz M, Agmon I, Kessler M, Weinstein S, Pioletti M, Avila H, Simitsopoulou M, Franceschi F, Janell D, Schluenzen F, Gluehmann M, Harms J, Hansen H, Tocilji A, Bennett W, Auerbach T, Yonath A. 2000. Identification of Selected Ribosomal Components in Crystallographic Maps of Prokaryotic Ribosomal Subunits at Medium Resolution, p 21-33. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch3
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Image of Figure 6
Figure 6

(a) Packing diagram of T50S, assembled by positioning the EM-reconstructed image ( ) in the crystallographic unit cell according to the unique prominent result of the molecular replacement search. A total of 11,000 unique reflections (to 9-Å resolution) were collected from native and TaBr-derivatized crystals. Six heavy-atom sites were extracted from anomalous-difference Patterson maps (FOM = 0.7188; = 0.75; phasing power = 1.56). (b) The most prominent TaBr sites are shown as golden balls (group scatterers with artificial diameters of about 6 Å ).

Citation: Bashan A, Bartels H, Levin I, Peretz M, Agmon I, Kessler M, Weinstein S, Pioletti M, Avila H, Simitsopoulou M, Franceschi F, Janell D, Schluenzen F, Gluehmann M, Harms J, Hansen H, Tocilji A, Bennett W, Auerbach T, Yonath A. 2000. Identification of Selected Ribosomal Components in Crystallographic Maps of Prokaryotic Ribosomal Subunits at Medium Resolution, p 21-33. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch3
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Tables

Generic image for table
Table 1

Crystals of ribosomal particles suitable for crystallographic studies

Citation: Bashan A, Bartels H, Levin I, Peretz M, Agmon I, Kessler M, Weinstein S, Pioletti M, Avila H, Simitsopoulou M, Franceschi F, Janell D, Schluenzen F, Gluehmann M, Harms J, Hansen H, Tocilji A, Bennett W, Auerbach T, Yonath A. 2000. Identification of Selected Ribosomal Components in Crystallographic Maps of Prokaryotic Ribosomal Subunits at Medium Resolution, p 21-33. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch3

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