Abstract

The small-subunit processome represents the earliest stable precursor of the eukaryotic small ribosomal subunit. Here we present the cryo-EM structure of the Saccharomyces cerevisiae small-subunit processome at an overall resolution of 3.8 Å, which provides an essentially complete near-atomic model of this assembly. In this nucleolar superstructure, 51 ribosome-assembly factors and two RNAs encapsulate the 18S rRNA precursor and 15 ribosomal proteins in a state that precedes pre-rRNA cleavage at site A1. Extended flexible proteins are employed to connect distant sites in this particle. Molecular mimicry and steric hindrance, as well as protein- and RNA-mediated RNA remodeling, are used in a concerted fashion to prevent the premature formation of the central pseudoknot and its surrounding elements within the small ribosomal subunit.

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Acknowledgements

We thank M. Ebrahim and J. Sotiris for outstanding support with data collection at the Evelyn Gruss Lipper Cryo-EM resource center at The Rockefeller University. We further thank T. Walz, G. Alushin and Y. Shi for helpful discussions. J.B. is supported by an EMBO long-term fellowship (ALTF 51-2014) and a Swiss National Science Foundation fellowship (155515), M.C.-M. is supported by a postgraduate scholarship from the Natural Sciences and Engineering Research Council of Canada (NSERC) and S.K. is supported by the Robertson Foundation, the Alfred P. Sloan Foundation, the Irma T. Hirschl Trust, the Alexandrine and Alexander L. Sinsheimer Fund, the Human Frontier Science Program Career Development Award and the NIH New Innovator Award (1DP2GM123459). B.T.C. is supported by National Institute of Health grant nos. P41GM103314 and P41GM109824.

Author information

Author notes

    • Jonas Barandun
    • , Malik Chaker-Margot
    •  & Mirjam Hunziker

    These authors contributed equally to this work.

Affiliations

  1. Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York, USA.

    • Jonas Barandun
    • , Malik Chaker-Margot
    • , Mirjam Hunziker
    •  & Sebastian Klinge
  2. Tri-Institutional Training Program in Chemical Biology, The Rockefeller University, New York, New York, USA.

    • Malik Chaker-Margot
  3. Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA.

    • Kelly R Molloy
    •  & Brian T Chait

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Contributions

S.K. established purification conditions, and M.C.-M. and J.B. acquired cryo-EM data. K.R.M. performed MS experiments and analyzed the resulting data with B.T.C. J.B., M.C.-M., M.H. and S.K. determined the cryo-EM structure of the yeast SSU processome, built the atomic model, interpreted the results and wrote the manuscript. All authors edited the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Sebastian Klinge.

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    Supplementary Text and Figures

    Supplementary Figures 1–10, Supplementary Table 1 and Supplementary Notes 1–21.

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    Life Sciences Reporting Summary

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    DSS-cross-links of the SSU processome.

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    Supplementary Data Set 2

    PyMOL session for the structural analysis of the SSU processome.

Videos

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    360° view of the cryo-EM reconstruction of the S. cerevisiae SSU processome.

    360° rotation of a composite cryo-EM map consisting of the 3.6 Å core, the 4.1 Å head-focused, the 4.1 Å 3′ domain and the 7.2 Å central domain maps. Densities for SSU processome components are color-coded. The rotation is paused at the same views as shown in Fig. 1 (0°, 120° and 240°) and labels for individual subunits are displayed. Subunits of complexes are shown in shades of blue (UtpA), red (UtpB), purple (U3 snoRNP), brown (Nop14/Noc4) and light-pink (Bms1-Rcl1). Ribosomal proteins are depicted in shades of grey. RNAs are colored in yellow (5′ ETS), red (U3 snoRNA) and white (pre-18S rRNA).

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DOI

https://doi.org/10.1038/nsmb.3472

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