A big step forward with the molecular magnifying glass…

Abstract

An impressive example of how structural methods advance our understanding of fundamental cell-biological processes is demonstrated by two recent papers in Cell [1xStructure of the 80S ribosome from Saccharomyces cerevisiae – tRNA–ribosome and subunit–subunit interactions. Spahn, C.M.T. et al. Cell. 2001; 107: 373–386Abstract | Full Text | Full Text PDF | PubMed | Scopus (379)See all References, 2xArchitecture of the protein-conducting channel associated with the translating 80S ribosome. Beckmann, R. et al. Cell. 2001; 107: 361–372Abstract | Full Text | Full Text PDF | PubMed | Scopus (283)See all References]. In a collaborative effort involving several laboratories, mainly those of Gunter Blobel and Joachim Frank, the structure of the 80S ribosome from the yeast Saccharomyces cerevisiae [1xStructure of the 80S ribosome from Saccharomyces cerevisiae – tRNA–ribosome and subunit–subunit interactions. Spahn, C.M.T. et al. Cell. 2001; 107: 373–386Abstract | Full Text | Full Text PDF | PubMed | Scopus (379)See all References[1] and the architecture of the associated protein-conducting channel of the endoplasmic reticulum [2xArchitecture of the protein-conducting channel associated with the translating 80S ribosome. Beckmann, R. et al. Cell. 2001; 107: 361–372Abstract | Full Text | Full Text PDF | PubMed | Scopus (283)See all References[2] have been analyzed at a molecular level.In the work by Spahn et al. [1xStructure of the 80S ribosome from Saccharomyces cerevisiae – tRNA–ribosome and subunit–subunit interactions. Spahn, C.M.T. et al. Cell. 2001; 107: 373–386Abstract | Full Text | Full Text PDF | PubMed | Scopus (379)See all References[1], cryo-EM reconstructions of the translating 80S ribosome at 15.4 A resolution, combined with separate models for ribosomal RNA and proteins, when available, were used to gain structural information on this protein-synthesizing machine. Although significant structural information on bacterial and archaebacterial ribosomes has been gleaned lately, very little was known about the structure of the eukaryotic counterpart. In fact, comparison of the newly dissected structure with those from lower organisms revealed that both the subunit contacts and the ribosome–tRNA interactions are remarkably conserved, suggesting a high degree of similarity in the mechanism of protein synthesis in the different systems. From the wealth of detailed structural information, some differences between the yeast and bacterial ribosomes became obvious. These are mainly attributed to the extended rRNA – so-called expansion elements – and some additional proteins in the yeast ribosome. Thus, four new subunit bridges were identified. Because most of these differences are not related in space to the prominent functional sites of the ribosome, but rather located on the surface of the particle, it was inferred that these eukaryote-specific elements might be important for interactions with other cellular components, perhaps in the context of ribosome dynamics and regulation.The paper by Beckmann et al. [2xArchitecture of the protein-conducting channel associated with the translating 80S ribosome. Beckmann, R. et al. Cell. 2001; 107: 361–372Abstract | Full Text | Full Text PDF | PubMed | Scopus (283)See all References[2] extends the scope of its companion by investigating the structure of the yeast protein-conducting channel in the ER and its interaction with the ribosome. A similar methodology to that in the first paper was applied, using immunopurified yeast ribosome–nascent chain complexes assembled in vitro and then reconstituted with the isolated Sec61 complex that serves as a protein-conducting channel in the ER. Cryo-EM reconstruction and modeling of active complexes having a tRNA bound at the P site showed four interactions of ribosomal RNA and proteins with the channel, as well as a ∼15 A gap between the large ribosomal subunit and the channel.Interestingly, in contrast to earlier models, the diameter of the translocation pore, formed by a Sec61 trimer, was estimated to be ∼15 A in both the inactive and active complexes, the latter being associated with a nascent chain containing a signal peptide. This compact conformation of the translocation channel led to the proposal of a simplified binary mode of cotranslational translocation. How far this model can be generalized remains to be seen – we'll have to wait for this approach to be applied to different types of translocated proteins.