Structure of the Escherichia coli ribosomal termination complex with release factor 2

Abstract

Termination of protein synthesis1 occurs when the messenger RNA presents a stop codon in the ribosomal aminoacyl (A) site. Class I release factor proteins (RF1 or RF2) are believed to recognize stop codons via tripeptide motifs2, leading to release of the completed polypeptide chain from its covalent attachment to transfer RNA in the ribosomal peptidyl (P) site. Class I RFs possess a conserved GGQ amino-acid motif that is thought to be involved directly in protein–transfer-RNA bond hydrolysis3,4. Crystal structures of bacterial and eukaryotic class I RFs have been determined5,6, but the mechanism of stop codon recognition and peptidyl-tRNA hydrolysis remains unclear. Here we present the structure of the Escherichia coli ribosome in a post-termination complex with RF2, obtained by single-particle cryo-electron microscopy (cryo-EM). Fitting the known 70S and RF2 structures into the electron density map reveals that RF2 adopts a different conformation on the ribosome when compared with the crystal structure of the isolated protein. The amino-terminal helical domain of RF2 contacts the factor-binding site of the ribosome, the ‘SPF’ loop of the protein is situated close to the mRNA, and the GGQ-containing domain of RF2 interacts with the peptidyl-transferase centre (PTC). By connecting the ribosomal decoding centre with the PTC, RF2 functionally mimics a tRNA molecule in the A site. Translational termination in eukaryotes is likely to be based on a similar mechanism.

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Figure 1: Stereo views of the structure of the post-termination complex revealing the location of release factor RF2.
Figure 2: Detailed stereo views of RF2–ribosome interactions at the level of the decoding site and the PTC.
Figure 3: The derived in situ RF2 structure and its interaction pattern.

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Acknowledgements

We thank M. Kjeldgaard for making the RF2 coordinates available before deposition; E. Murgola for sharing data before publication; E. Morris, R. Finn and R. Matadeen for discussions on image processing; M. Schatz and R. Schmidt for improvements to the IMAGIC software system; G. Willoughby for computational support; and R. Brimacombe for discussions. This work was supported in part by grants from the BBSRC and the EU. B.V. was funded by the NIH. A.V.Z. and M.E. were supported by the Swedish Foundation for Strategic Research and the Swedish Research Council.

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Correspondence to Marin van Heel.

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M.v.H. is a shareholder of Image Science Software GmbH, distributors of the IMAGIC-5 software.

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Klaholz, B., Pape, T., Zavialov, A. et al. Structure of the Escherichia coli ribosomal termination complex with release factor 2. Nature 421, 90–94 (2003). https://doi.org/10.1038/nature01225

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