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Time-resolved cryo-EM visualizes ribosomal translocation with EF-G and GTP

Author

Listed:
  • Christine E. Carbone

    (UMass Chan Medical School)

  • Anna B. Loveland

    (UMass Chan Medical School)

  • Howard B. Gamper

    (Thomas Jefferson University)

  • Ya-Ming Hou

    (Thomas Jefferson University)

  • Gabriel Demo

    (UMass Chan Medical School
    Masaryk University)

  • Andrei A. Korostelev

    (UMass Chan Medical School)

Abstract

During translation, a conserved GTPase elongation factor—EF-G in bacteria or eEF2 in eukaryotes—translocates tRNA and mRNA through the ribosome. EF-G has been proposed to act as a flexible motor that propels tRNA and mRNA movement, as a rigid pawl that biases unidirectional translocation resulting from ribosome rearrangements, or by various combinations of motor- and pawl-like mechanisms. Using time-resolved cryo-EM, we visualized GTP-catalyzed translocation without inhibitors, capturing elusive structures of ribosome•EF-G intermediates at near-atomic resolution. Prior to translocation, EF-G binds near peptidyl-tRNA, while the rotated 30S subunit stabilizes the EF-G GTPase center. Reverse 30S rotation releases Pi and translocates peptidyl-tRNA and EF-G by ~20 Å. An additional 4-Å translocation initiates EF-G dissociation from a transient ribosome state with highly swiveled 30S head. The structures visualize how nearly rigid EF-G rectifies inherent and spontaneous ribosomal dynamics into tRNA-mRNA translocation, whereas GTP hydrolysis and Pi release drive EF-G dissociation.

Suggested Citation

  • Christine E. Carbone & Anna B. Loveland & Howard B. Gamper & Ya-Ming Hou & Gabriel Demo & Andrei A. Korostelev, 2021. "Time-resolved cryo-EM visualizes ribosomal translocation with EF-G and GTP," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-27415-0
    DOI: 10.1038/s41467-021-27415-0
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    References listed on IDEAS

    as
    1. Anna B. Loveland & Gabriel Demo & Andrei A. Korostelev, 2020. "Cryo-EM of elongating ribosome with EF-Tu•GTP elucidates tRNA proofreading," Nature, Nature, vol. 584(7822), pages 640-645, August.
    2. Andreas H. Ratje & Justus Loerke & Aleksandra Mikolajka & Matthias Brünner & Peter W. Hildebrand & Agata L. Starosta & Alexandra Dönhöfer & Sean R. Connell & Paola Fucini & Thorsten Mielke & Paul C. W, 2010. "Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites," Nature, Nature, vol. 468(7324), pages 713-716, December.
    3. Joachim Frank & Rajendra Kumar Agrawal, 2000. "A ratchet-like inter-subunit reorganization of the ribosome during translocation," Nature, Nature, vol. 406(6793), pages 318-322, July.
    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.
    5. Natalia Demeshkina & Lasse Jenner & Eric Westhof & Marat Yusupov & Gulnara Yusupova, 2012. "A new understanding of the decoding principle on the ribosome," Nature, Nature, vol. 484(7393), pages 256-259, April.
    6. Gabriel Demo & Howard B. Gamper & Anna B. Loveland & Isao Masuda & Christine E. Carbone & Egor Svidritskiy & Ya-Ming Hou & Andrei A. Korostelev, 2021. "Structural basis for +1 ribosomal frameshifting during EF-G-catalyzed translocation," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    7. Emily J. Rundlet & Mikael Holm & Magdalena Schacherl & S. Kundhavai Natchiar & Roger B. Altman & Christian M. T. Spahn & Alexander G. Myasnikov & Scott C. Blanchard, 2021. "Structural basis of early translocation events on the ribosome," Nature, Nature, vol. 595(7869), pages 741-745, July.
    8. Marina V. Rodnina & Andreas Savelsbergh & Vladimir I. Katunin & Wolfgang Wintermeyer, 1997. "Hydrolysis of GTP by elongation factor G drives tRNA movement on the ribosome," Nature, Nature, vol. 385(6611), pages 37-41, January.
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