Structure of the 30S translation initiation complex

Abstract

Translation initiation, the rate-limiting step of the universal process of protein synthesis, proceeds through sequential, tightly regulated steps. In bacteria, the correct messenger RNA start site and the reading frame are selected when, with the help of initiation factors IF1, IF2 and IF3, the initiation codon is decoded in the peptidyl site of the 30S ribosomal subunit by the fMet-tRNAfMet anticodon. This yields a 30S initiation complex (30SIC) that is an intermediate in the formation of the 70S initiation complex (70SIC) that occurs on joining of the 50S ribosomal subunit to the 30SIC and release of the initiation factors1,2,3. The localization of IF2 in the 30SIC has proved to be difficult so far using biochemical approaches, but could now be addressed using cryo-electron microscopy and advanced particle separation techniques on the basis of three-dimensional statistical analysis. Here we report the direct visualization of a 30SIC containing mRNA, fMet-tRNAfMet and initiation factors IF1 and GTP-bound IF2. We demonstrate that the fMet-tRNAfMet is held in a characteristic and precise position and conformation by two interactions that contribute to the formation of a stable complex: one involves the transfer RNA decoding stem which is buried in the 30S peptidyl site, and the other occurs between the carboxy-terminal domain of IF2 and the tRNA acceptor end. The structure provides insights into the mechanism of 70SIC assembly and rationalizes the rapid activation of GTP hydrolysis triggered on 30SIC–50S joining2,3 by showing that the GTP-binding domain of IF2 would directly face the GTPase-activated centre of the 50S subunit.

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Figure 1: One sample—several structures.
Figure 2: Fitting and map interpretation of the 30SIC.
Figure 3: Comparisons of the tRNA and IF2 positions in different translation initiation complexes, and model of ribosomal subunit joining.

Accession codes

Primary accessions

EMBL/GenBank/DDBJ

Data deposits

The electron density map of the 30SIC complex has been deposited to the EM Data Bank under the accession number EMD-1523.

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Acknowledgements

We thank J. Thompson for providing IF2 strains, M. Argentini for mass spectroscopy analysis of IF1 and IF2, and P. Schultz, D. Moras, J.-C. Thierry, V. Mallouh, G. Yusupova and I. Orlov for their constant support and interest. This work was supported by grants from the Centre National pour la Recherche Scientifique (CNRS), the Ministère de la Recherche et de la Technologie, the European Molecular Biology Organization Young Investigator Programme, the Institut du Développement et des Ressources en Informatique Scientifique, and the European Commission as SPINE2-complexes (contract no LSHG-CT-2006-031220). A.S. is a PhD student in a co-tutorial between the Université Louis Pasteur (ULP) and the Università di Camerino, and was supported by SPINE2-complexes, by the Institut National de la Santé et de la Recherche Médicale (INSERM) and by the Fondation de la Recherche Médicale (FRM). S.M. was supported by postdoctoral fellowships from the ULP, the CNRS and from the FRM, and A.G.M. was a recipient of postdoctoral fellowships from the CNRS and the FRM. The electron microscope facility is supported by the Alsace Region, the INSERM, the CNRS and the Association pour la Recherche sur le Cancer.

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Correspondence to Bruno P. Klaholz.

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Simonetti, A., Marzi, S., Myasnikov, A. et al. Structure of the 30S translation initiation complex. Nature 455, 416–420 (2008). https://doi.org/10.1038/nature07192

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