The triplet-based genetic code requires that translating ribosomes maintain the reading frame of a messenger RNA faithfully to ensure correct protein synthesis1. However, in programmed -1 ribosomal frameshifting2, a specific subversion of frame maintenance takes place, wherein the ribosome is forced to shift one nucleotide backwards into an overlapping reading frame and to translate an entirely new sequence of amino acids. This process is indispensable in the replication of numerous viral pathogens, including HIV and the coronavirus associated with severe acute respiratory syndrome3, and is also exploited in the expression of several cellular genes4. Frameshifting is promoted by an mRNA signal composed of two essential elements: a heptanucleotide ‘slippery’ sequence5 and an adjacent mRNA secondary structure, most often an mRNA pseudoknot6. How these components operate together to manipulate the ribosome is unknown. Here we describe the observation of a ribosome–mRNA pseudoknot complex that is stalled in the process of -1 frameshifting. Cryoelectron microscopic imaging of purified mammalian 80S ribosomes from rabbit reticulocytes paused at a coronavirus pseudoknot reveals an intermediate of the frameshifting process. From this it can be seen how the pseudoknot interacts with the ribosome to block the mRNA entrance channel, compromising the translocation process and leading to a spring-like deformation of the P-site transfer RNA. In addition, we identify movements of the likely eukaryotic ribosomal helicase and confirm a direct interaction between the translocase eEF2 and the P-site tRNA. Together, the structural changes provide a mechanical explanation of how the pseudoknot manipulates the ribosome into a different reading frame.
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I.B. thanks P. Farabaugh for helpful discussions. This work was supported by grants from the Biotechnology and Biological Sciences Research Council, UK, and the Medical Research Council, UK. S.J.M. holds a Wellcome Trust Structural Biology Studentship, D.I.S. is an MRC Research Professor, and R.J.C.G. is a Royal Society University Research Fellow. Author Contributions O.N. and S.J.M. contributed equally to this work. O.N. and I.B. purified the stalled ribosome complexes; S.J.M., D.I.S. and R.J.C.G. solved the structures. All authors discussed the results and contributed to writing of the manuscript.
This file contains Supplementary Figures 1 and 2, Supplementary Methods and Supplementary Notes. Of the two supplementary figures, one illustrates the purification of stalled ribosomes, the other a stereoview of the small subunit of the pseudoknot-stalled complex.