1. Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch cedex, France
2. These authors contributed equally to this work.

Correspondence to: Marat Yusupov¹ Coordinates and structure factors have been deposited in the Protein Data Bank under accession numbers 2HGR and 2HGU (initiation complex 30S and 50S subunits), 2HGP and 2HGQ (post-initiation complex) and 2HGI and 2HGJ (mRNA-free complex). Correspondence and requests for materials should be addressed to M.Y. (Email: marat@titus.u-strasbg.fr).

Abstract

Translation initiation is a major determinant of the overall expression level of a gene^{1, 2, 3}. The translation of functionally active protein requires the messenger RNA to be positioned on the ribosome such that the start/initiation codon will be read first and in the correct frame. Little is known about the molecular basis for the interaction of mRNA with the ribosome at different states of translation. Recent crystal structures of the ribosomal subunits^{4, 5, 6, 7, 8}, the empty 70S ribosome⁹ and the 70S ribosome containing functional ligands^{10, 11, 12, 13} have provided information about the general organization of the ribosome and its functional centres. Here we compare the X-ray structures of eight ribosome complexes modelling the translation initiation, post-initiation and elongation states. In the initiation and post-initiation complexes, the presence of the Shine–Dalgarno (SD) duplex causes strong anchoring of the 5'-end of mRNA onto the platform of the 30S subunit, with numerous interactions between mRNA and the ribosome. Conversely, the 5' end of the 'elongator' mRNA lacking SD interactions is flexible, suggesting a different exit path for mRNA during elongation. After the initiation of translation, but while an SD interaction is still present, mRNA moves in the 3'5' direction with simultaneous clockwise rotation and lengthening of the SD duplex, bringing it into contact with ribosomal protein S2.

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