A comparison of the yeast and rabbit 80 S ribosome reveals the topology ofthe nascent chain exit tunnel, inter-subunit bridges and mammalian rRNA expansion segments

Protein synthesis in eukaryotes is mediated by both cytoplasmic and membran e-bound ribosomes. During the co-translational translocation of secretory a nd membrane proteins, eukaryotic ribosomes dock with the protein conducting channel of the endoplasmic reticulum. An understanding of these processes will require the detailed structure of a eukaryotic ribosome. To this end, we have compared the three-dimensional structures of yeast and rabbit ribos omes at 24 Angstrom resolution. In general, we find that the active sites f or protein synthesis and translocation have been highly conserved. It is in teresting that a channel was visualized in the neck of the small subunit wh ose entrance is formed by a deep groove. By analogy with the prokaryotic sm all subunit, this channel may provide a conserved portal through which mRNA is threaded into the decoding center. In addition, both the small and larg e subunits are built around a dense tubular network. Our analysis further s uggests that the nascent chain exit tunnel and the docking surface for the endoplasmic reticulum channel are formed by this network. We surmise that m any of these features correspond to rRNA, based on biochemical and structur al data. Ribosomal function is critically dependent on the specific association of s mall and large subunits. Our analysis of eukaryotic ribosomes reveals four conserved inter-subunit bridges with a geometry similar to that found in pr okaryotes. In particular, a double-bridge connects the small subunit platfo rm with the interface canyon on the large subunit. Moreover, a novel bridge is formed between the platform and the base of the L1 domain. Finally, siz e differences between mammalian and yeast large subunit rRNAs have been cor related with five expansion segments that form two large spines and three e xtended fingers. Overall, we find that expansion segments within the large subunit rRNA have been incorporated at positions distinct from the active s ites for protein synthesis and translocation. (C) 2000 Academic Press.