Mammalian (rat) ribosomes have 80 proteins; the sequence of amino acids in 75 have been determined. What has been learned of the structure of the rat ribosomal proteins is reviewed with particular attention to their evolution and to amino acid sequence motifs. The latter include: clusters of basic or acidic residues; sequence repeats or shared sequences; zinc finger domains; bZIP elements; and nuclear localization signals. The occurrence and the possible significance of phosphorylated residues and of ubiquitin extensions is noted. The characteristics of the mRNAs that encode the proteins are summarized. The relationship of the rat ribosomal proteins to the proteins in ribosomes from humans, yeast, archaebacteria, and Escherichia coli is collated.

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The structure of a 29-nucleotide RNA containing the sarcin͞ricin loop (SRL) of rat 28 S rRNA has been determined at 2.1 Å resolution. Recognition of the SRL by elongation factors and by the ribotoxins, sarcin and ricin, requires a nearly universal dodecamer sequence that folds into a G-bulged cross-strand A stack and a GAGA tetraloop. The juxtaposition of these two motifs forms a distorted hairpin structure that allows direct recognition of bases in both grooves as well as recognition of nonhelical backbone geometry and two 5-unstacked purines. Comparisons with other RNA crystal structures establish the cross-strand A stack and the GNRA tetraloop as defined and modular RNA structural elements. The conserved region at the top is connected to the base of the domain by a region presumed to be f lexible because of the sparsity of stabilizing contacts. Although the conformation of the SRL RNA previously determined by NMR spectroscopy is similar to the structure determined by x-ray crystallography, significant differences are observed in the ''f lexible'' region and to a lesser extent in the G-bulged cross-strand A stack.The highly conserved sarcin͞ricin loop (SRL), a component of 23-28 S rRNA, is essential for protein synthesis because it participates in the binding of elongation factors (EFs) to the ribosome. The function of this domain was illucidated by studying ribosomes treated with its namesake ribotoxins, sarcin and ricin (1, 2). The ribotoxins cleave a single covalent bond in the SRL RNA, which kill cells by inactivating ribosomes. Sarcin is a ribonuclease that cleaves the phosphodiester backbone on the 3Ј-side of G4325 (rat 28 S rRNA numbering is used throughout) (1, 2). Ricin depurinates the 5Ј-adjacent A4324 (3). EF-dependent functions are specifically impaired when ribosomes are treated with either toxin, whereas other ribosomal functions including EF-G-independent translocation are unaffected (1). Further indications of the domain's importance are that 12 of its 17 nucleotides are near universal and that chemical footprinting (4) marks it as the only rRNA region protected by both EFs.An SRL RNA can mimic the SRL in the ribosome because binding of EF-G to an Escherichia coli or rat SRL RNA is only Ϸ10-fold weaker than binding to intact E. coli ribosomes (5). Further, only the GTP-bound and apoprotein forms of EF-G bind the E. coli SRL RNA, whereas GDP-bound EF-G does not (5). EF-G binding is most affected by mutation of G4319 (5). Both toxins recognize and cleave a single bond in the SRL oligonucleotide (Fig. 1). Comprehensive mutational analysis of the SRL established that sarcin recognition and cleavage are largely dependent on a single base, the bulged G4319 (7). In contrast, each of the 4 nt of the GAGA tetraloop is necessary, and a GAGA tetraloop is sufficient for ricin recognition and depurination (6).The perception of RNA loop structure was altered by the determination of the conformation of the rat SRL by NMR spectroscopy (8, 9). Because the rules that govern formation of non-Watson-Crick ...

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