Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome

  1. Priyanka D Abeyrathne
  2. Cha San Koh
  3. Timothy Grant
  4. Nikolaus Grigorieff
  5. Andrei A Korostelev  Is a corresponding author
  1. Janelia Research Campus, Howard Hughes Medical Institute, United States
  2. University of Massachusetts Medical School, United States

Abstract

Internal ribosome entry sites (IRESs) mediate cap-independent translation of viral mRNAs. Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the Taura syndrome virus IRES and translocase eEF2•GTP bound with sordarin. The structures suggest a trajectory of IRES translocation, required for translation initiation, and provide an unprecedented view of eEF2 dynamics. The IRES rearranges from extended to bent to extended conformations. This inchworm-like movement is coupled with ribosomal inter-subunit rotation and 40S head swivel. eEF2, attached to the 60S subunit, slides along the rotating 40S subunit to enter the A site. Its diphthamide-bearing tip at domain IV separates the tRNA-mRNA-like pseudoknot I (PKI) of the IRES from the decoding center. This unlocks 40S domains, facilitating head swivel and biasing IRES translocation via hitherto-elusive intermediates with PKI captured between the A and P sites. The structures suggest missing links in our understanding of tRNA translocation.

Article and author information

Author details

  1. Priyanka D Abeyrathne

    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    Competing interests
    No competing interests declared.
  2. Cha San Koh

    RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    No competing interests declared.
  3. Timothy Grant

    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    Competing interests
    No competing interests declared.
  4. Nikolaus Grigorieff

    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    Competing interests
    Nikolaus Grigorieff, Reviewing editor, eLife.
  5. Andrei A Korostelev

    RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
    For correspondence
    andrei.korostelev@umassmed.edu
    Competing interests
    No competing interests declared.

Reviewing Editor

  1. Sriram Subramaniam, National Cancer Institute, United States

Version history

  1. Received: February 1, 2016
  2. Accepted: May 8, 2016
  3. Accepted Manuscript published: May 9, 2016 (version 1)
  4. Version of Record published: June 7, 2016 (version 2)

Copyright

© 2016, Abeyrathne et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Priyanka D Abeyrathne
  2. Cha San Koh
  3. Timothy Grant
  4. Nikolaus Grigorieff
  5. Andrei A Korostelev
(2016)
Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome
eLife 5:e14874.
https://doi.org/10.7554/eLife.14874

Share this article

https://doi.org/10.7554/eLife.14874

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