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Structural basis for translation termination on the 70S ribosome

Abstract

At termination of protein synthesis, type I release factors promote hydrolysis of the peptidyl-transfer RNA linkage in response to recognition of a stop codon. Here we describe the crystal structure of the Thermus thermophilus 70S ribosome in complex with the release factor RF1, tRNA and a messenger RNA containing a UAA stop codon, at 3.2 Å resolution. The stop codon is recognized in a pocket formed by conserved elements of RF1, including its PxT recognition motif, and 16S ribosomal RNA. The codon and the 30S subunit A site undergo an induced fit that results in stabilization of a conformation of RF1 that promotes its interaction with the peptidyl transferase centre. Unexpectedly, the main-chain amide group of Gln 230 in the universally conserved GGQ motif of the factor is positioned to contribute directly to peptidyl-tRNA hydrolysis.

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Figure 1: Structure of RF1 in the termination complex.
Figure 2: Interactions with the UAA stop codon in the decoding centre of the RF1 termination complex.
Figure 3: Interactions of the GGQ region of RF1 in the PTC.
Figure 4: Stereo view of the RF1 binding pocket for 23S rRNA nucleotide A2602.
Figure 5: Rearrangements and packing of the switch loop of RF1.

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Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors have been deposited with the Protein Data Bank under accession codes 3D5A, 3D5B, 3D5C and 3D5D.

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Acknowledgements

We thank B. Scott for his input through many stages of this work, and D. Ermolenko, L. Horan, L. Lancaster, B. Scott and D. Staple for comments on the manuscript. We are grateful to the beamline staff at SSRL, ALS and APS for their support during screening and data collection, and to Crystal Chan for her help in using the Berkeley Fermentation Facility. This work was supported by grants from the NIH and NSF (to H.F.N.) and by a fellowship from the Danish Research Council (to M.L.).

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Correspondence to Harry F. Noller.

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This file contains Supplementary Methods, Supplementary Table S1, Supplementary Figures S1-S11 and References. (PDF 1769 kb)

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Laurberg, M., Asahara, H., Korostelev, A. et al. Structural basis for translation termination on the 70S ribosome. Nature 454, 852–857 (2008). https://doi.org/10.1038/nature07115

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