Molecular Architecture of a Late 40S Ribosome Assembly Intermediate

Ribosomes are self-assembling macromolecular machines which catalyze the synthesis of proteins in all cells, and are made up of two subunits that differ in size due to the presence of RNA and proteins in different ratio. Although significant structural details of the organization of mature ribosomes in prokaryotes and eukaryotes have been elucidated in the past decade, ribosome biogenesis and assembly processes are poorly understood. Ribosome assembly in eukaryotes requires at least 200 essential transiently associating assembly factor proteins that facilitate the RNA folding and recruitment of ribosomal proteins. We have determined the structure of a late cytoplasmic 40S ribosome assembly intermediate from Saccharomyces Cerevisiae with the help of Cryo-electron microscopy and multiscale molecular simulation techniques. We have collected maps of the immature 40S particles and its components at various resolutions, and apply molecular dynamics based flexible fitting (MDFF) to fit an initial atomic model in to the cryo-EM maps of immature 40S particles with minimal structural perturbation. We verify that the largest conformational change observed in RNA can be robustly  generated with an independent technique called normal mode flexible fitting (NMFF). We find that the pre-40s particles in addition to ribosomal RNA and proteins also contain 7 types of assembly factors, the joint activity of which blocks the translation initiation pathway in immature 40S subunits.