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Visualization of codon-dependent conformational rearrangements during translation termination

Nature Structural & Molecular Biology volume 17, pages 465–470 (2010)Cite this article

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Abstract

Although the recognition of stop codons by class 1 release factors (RFs) on the ribosome takes place with extremely high fidelity, the molecular mechanisms behind this remarkable process are poorly understood. Here we performed structural probing experiments with Fe(II)-derivatized RFs to compare the conformations of cognate and near-cognate ribosome termination complexes. The structural differences that we document provide an unprecedented view of how authentic stop-codon recognition is signaled to the large subunit of the ribosome. These events initiate with very close interactions between RF and the small-subunit decoding center, lead to increased interactions between the switch loop of the RF and specific regions of the subunit interface and end in the adoption of the precise orientation of the RF for maximal catalytic activity in the large-subunit peptidyl transferase center.

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Figure 1: Directed hydroxyl radical probing of the interaction between the codon-recognition domain of RF1 and the ribosome in complexes programmed with various codons in the A site.
Figure 2: Directed hydroxyl radical probing of the ribosome environment of the switch loop of RF1 in ribosome complexes programmed with various codons in the A site.
Figure 3: Directed hydroxyl radical probing of the ribosome environment of the catalytic motif Gly-Gly-Gln of RF1 in ribosome complexes programmed with various codons in the A site.
Figure 4: Cartoon representation of structural rearrangements in ribosome complexes.

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Acknowledgements

We thank E. Youngman, H. Zaher, S. Djuranovic and N. Guydosh for comments on the manuscript, the US National Institutes of Health for funding of the project and the Howard Hughes Medical Institute for salary support to R.G.

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Authors and Affiliations

  1. Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    Shan L He & Rachel Green

  2. Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

    Shan L He & Rachel Green

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  1. Shan L He
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  2. Rachel Green
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Contributions

S.L.H. and R.G. designed the experiments; S.L.H. performed the experiments; S.L.H. and R.G. discussed results and contributed to the manuscript.

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Correspondence to Rachel Green.

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The authors declare no competing financial interests.

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He, S., Green, R. Visualization of codon-dependent conformational rearrangements during translation termination. Nat Struct Mol Biol 17, 465–470 (2010). https://doi.org/10.1038/nsmb.1766

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