Letter | Published:

Structural basis for stop codon recognition in eukaryotes

Nature volume 524, pages 493496 (27 August 2015) | Download Citation

Abstract

Termination of protein synthesis occurs when a translating ribosome encounters one of three universally conserved stop codons: UAA, UAG or UGA. Release factors recognize stop codons in the ribosomal A-site to mediate release of the nascent chain and recycling of the ribosome. Bacteria decode stop codons using two separate release factors with differing specificities for the second and third bases1. By contrast, eukaryotes rely on an evolutionarily unrelated omnipotent release factor (eRF1) to recognize all three stop codons2. The molecular basis of eRF1 discrimination for stop codons over sense codons is not known. Here we present cryo-electron microscopy (cryo-EM) structures at 3.5–3.8 Å resolution of mammalian ribosomal complexes containing eRF1 interacting with each of the three stop codons in the A-site. Binding of eRF1 flips nucleotide A1825 of 18S ribosomal RNA so that it stacks on the second and third stop codon bases. This configuration pulls the fourth position base into the A-site, where it is stabilized by stacking against G626 of 18S rRNA. Thus, eRF1 exploits two rRNA nucleotides also used during transfer RNA selection to drive messenger RNA compaction. In this compacted mRNA conformation, stop codons are favoured by a hydrogen-bonding network formed between rRNA and essential eRF1 residues that constrains the identity of the bases. These results provide a molecular framework for eukaryotic stop codon recognition and have implications for future studies on the mechanisms of canonical and premature translation termination3,4.

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Accessions

Primary accessions

Electron Microscopy Data Bank

Data deposits

Maps have been deposited with the EMDB under accession codes 3038, 3039, and 3040. Atomic coordinates have been deposited with the Protein Data Bank under accession codes 3JAG, 3JAH and 3JAI.

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Acknowledgements

We thank C. Savva, F. de Haas, and S. Welsch for assisting with cryo-EM data collection, J. Grimmett and T. Darling for computing support, D. Barford for critically reading the manuscript, and I. Fernández, J. Llácer, G. Murshudov, S. Scheres, and R. Voorhees for useful discussions. Gctf is available on request from K. Zhang (kzhang@mrc-lmb.cam.ac.uk). This work was supported by the UK Medical Research Council (MC_UP_A022_1007 to R.S.H. and MC_U105184332 to V.R.). A.B. was supported by a Career Development Fellowship. S.S. was supported by a St John’s College Title A fellowship. J.M. thanks T. Dever, NICHD, and the NIH Oxford-Cambridge Scholars’ Program for support. V.R. was supported by a Wellcome Trust Senior Investigator award (WT096570), the Agouron Institute, and the Jeantet Foundation.

Author information

Author notes

    • Alan Brown
    •  & Sichen Shao

    These authors contributed equally to this work

Affiliations

  1. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK

    • Alan Brown
    • , Sichen Shao
    • , Jason Murray
    • , Ramanujan S. Hegde
    •  & V. Ramakrishnan

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Contributions

A.B., S.S., R.S.H. and V.R. designed the study. S.S. purified complexes and prepared samples. A.B., S.S. and J.M. collected data. A.B. calculated the cryo-EM reconstructions, built the atomic models and interpreted the structure. A.B., S.S., R.S.H and V.R. wrote the manuscript. All authors discussed and commented on the final manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Ramanujan S. Hegde or V. Ramakrishnan.

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https://doi.org/10.1038/nature14896

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