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Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy

Author

Listed:
  • Niels Fischer

    (3D Electron Cryomicroscopy Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany)

  • Andrey L. Konevega

    (Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
    Petersburg Nuclear Physics Institute)

  • Wolfgang Wintermeyer

    (Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany)

  • Marina V. Rodnina

    (Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany)

  • Holger Stark

    (3D Electron Cryomicroscopy Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany)

Abstract

The translocation step of protein synthesis entails large-scale rearrangements of the ribosome–transfer RNA (tRNA) complex. Here we have followed tRNA movement through the ribosome during translocation by time-resolved single-particle electron cryomicroscopy (cryo-EM). Unbiased computational sorting of cryo-EM images yielded 50 distinct three-dimensional reconstructions, showing the tRNAs in classical, hybrid and various novel intermediate states that provide trajectories and kinetic information about tRNA movement through the ribosome. The structures indicate how tRNA movement is coupled with global and local conformational changes of the ribosome, in particular of the head and body of the small ribosomal subunit, and show that dynamic interactions between tRNAs and ribosomal residues confine the path of the tRNAs through the ribosome. The temperature dependence of ribosome dynamics reveals a surprisingly flat energy landscape of conformational variations at physiological temperature. The ribosome functions as a Brownian machine that couples spontaneous conformational changes driven by thermal energy to directed movement.

Suggested Citation

  • Niels Fischer & Andrey L. Konevega & Wolfgang Wintermeyer & Marina V. Rodnina & Holger Stark, 2010. "Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy," Nature, Nature, vol. 466(7304), pages 329-333, July.
    • Handle: RePEc:nat:nature:v:466:y:2010:i:7304:d:10.1038_nature09206
    DOI: 10.1038/nature09206
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    Cited by:

    1. Lars V. Bock & Helmut Grubmüller, 2022. "Effects of cryo-EM cooling on structural ensembles," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    2. Do Hoon Kwon & Feng Zhang & Justin G. Fedor & Yang Suo & Seok-Yong Lee, 2022. "Vanilloid-dependent TRPV1 opening trajectory from cryoEM ensemble analysis," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    3. Panagiotis Poulis & Anoshi Patel & Marina V. Rodnina & Sarah Adio, 2022. "Altered tRNA dynamics during translocation on slippery mRNA as determinant of spontaneous ribosome frameshifting," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    4. Valentyn Petrychenko & Bee-Zen Peng & Ana C. A. P. Schwarzer & Frank Peske & Marina V. Rodnina & Niels Fischer, 2021. "Structural mechanism of GTPase-powered ribosome-tRNA movement," Nature Communications, Nature, vol. 12(1), pages 1-9, December.

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