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

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.

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The Ribosome: Structure, Function, Antibiotics, and Cellular Interactions