The ribosome is a large complex composed of two-thirds RNA and one-third protein. The determination, in 2000, of the entire three-dimensional conformation of its large and small subunits is a major triumph of modern structural biology. The findings confirm earlier evidence that rRNAs—and not proteins—are responsible for the ribosome’s overall structure, its ability to position tRNAs on the mRNA, and its catalytic activity in forming covalent peptide bonds. The ribosomal RNAs are folded into highly compact, precise three-dimensional structures that form the compact core of the ribosome and determine its overall shape (Figure 6–67).
In marked contrast to the central positions of the rRNAs, the ribosomal proteins are generally located on the surface and fill in the gaps and crevices of the folded RNA (Figure 6–68). Some of these proteins send out extended regions of polypeptide chain that penetrate short distances into holes in the RNA core (Figure 6–69). The main role of the ribosomal proteins seems to be to stabilize the
Figure 6–67 Structure of the rRNAs in the large subunit of a bacterial ribosome, as determined by x-ray crystallography. (A) Three-dimensional conformations of the large-subunit rRNAs (5S and 23S) as they appear in the ribosome. One of the protein subunits of the ribosome (L1) is also shown as a reference point, since it forms a characteristic protrusion on the ribosome. (B) Schematic diagram of the secondary structure of the 23S rRNA, showing the extensive network of base-pairing. The structure has been divided into six “domains” whose colors correspond to those in (A). The secondary-structure diagram is highly schematized to represent as much of the structure as possible in two dimensions. To do this, several discontinuities in the RNA chain have been introduced, although in reality the 23S rRNA is a single RNA molecule. For example, the base of Domain III is continuous with the base of Domain IV even though a gap appears in the diagram. (Adapted from N. Ban et al., Science 289:905–920, 2000. With permission  from AAAS.)
RNA core, while permitting the changes in rRNA conformation that are necessary for this RNA to catalyze efficient protein synthesis. The proteins also aid in the initial assembly of the rRNAs that make up the core of the ribosome.
Not only are the A, P, and E binding sites for tRNAs formed primarily by ribosomal RNAs, but the catalytic site for peptide bond formation is also formed by RNA, as the nearest amino acid is located more than 1.8 nm away. This discovery came as a surprise to biologists because, unlike proteins, RNA does not contain easily ionizable functional groups that can be used to catalyze sophisticated reactions like peptide bond formation. Moreover, metal ions, which are often used by RNA molecules to catalyze chemical reactions (as discussed later in the chapter), were not observed at the active site of the ribosome. Instead, it is believed that the 23S rRNA forms a highly structured pocket that, through a network of hydrogen bonds, precisely orients the two reactants (the growing peptide chain and an aminoacyl-tRNA) and thereby greatly accelerates their covalent joining. An additional surprise came from the discovery that the tRNA in the P site contributes an important OH group to the active site and participates directly in the catalysis. This mechanism may ensure that catalysis occurs only when the P site tRNA is properly positioned in the ribosome.