Structures of translationally inactive mammalian ribosomes
- Harvard Medical School, United States
- MRC Laboratory of Molecular Biology, United Kingdom
Abstract
The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. Here, we use electron cryomicroscopy to analyze inactive ribosomes isolated from mammalian reticulocytes, the penultimate stage of red blood cell differentiation. We identify two types of ribosomes that are translationally repressed by protein interactions. The first comprises ribosomes sequestered with elongation factor 2 (eEF2) by SERPINE mRNA binding protein 1 (SERBP1) occupying the ribosomal mRNA entrance channel. The second type are translationally repressed by a novel ribosome-binding protein, interferon-related developmental regulator 2 (IFRD2), which spans the P and E sites and inserts a C-terminal helix into the mRNA exit channel to preclude translation. IFRD2 binds ribosomes with a tRNA occupying a noncanonical binding site, the 'Z site', on the ribosome. These structures provide functional insights into how ribosomal interactions may suppress translation to regulate gene expression.
Data availability
All cryo-EM maps and models have been deposited in EMDB under accession codes 9234, 9235, 9236, 9237, 9239, 9240, 9241 and 9242. All models have been deposited in PDB under accession codes 6MTB, 6MTC, 6MTD and 6MTE.
-
Data from: Structures of translationally inactive mammalian ribosomesPublicly available at the EMBL-EBI Protein Data Bank (accession no: EMD-9234).
-
Data from: Structures of translationally inactive mammalian ribosomesPublicly available at the EMBL-EBI Protein Data Bank (accession no: EMD-9235).
-
Data from: Structures of translationally inactive mammalian ribosomesPublicly available at the EMBL-EBI Protein Data Bank (accession no: EMD-9236).
-
Data from: Structures of translationally inactive mammalian ribosomesPublicly available at the EMBL-EBI Protein Data Bank (accession no: EMD-9237).
-
Data from: Structures of translationally inactive mammalian ribosomesPublicly available at the EMBL-EBI Protein Data Bank (accession no: EMD-9239).
-
Data from: Structures of translationally inactive mammalian ribosomesPublicly available at the EMBL-EBI Protein Data Bank (accession no: EMD-9240).
-
Data from: Structures of translationally inactive mammalian ribosomesPublicly available at the EMBL-EBI Protein Data Bank (accession no: EMD-9241).
-
Data from: Structures of translationally inactive mammalian ribosomesPublicly available at the EMBL-EBI Protein Data Bank (accession no: EMD-9242).
-
Data from: Structures of translationally inactive mammalian ribosomesPublicly available at the RCSB Protein Data Bank (accession no: 6MTB).
-
Data from: Structures of translationally inactive mammalian ribosomesPublicly available at the RCSB Protein Data Bank (accession no: 6MTC).
-
Data from: Structures of translationally inactive mammalian ribosomesPublicly available at the RCSB Protein Data Bank (accession no: 6MTD).
-
Data from: Structures of translationally inactive mammalian ribosomesPublicly available at the RCSB Protein Data Bank (accession no: 6MTE).
Article and author information
Author details
Funding
Harvard Medical School (N/A)
- Alan Brown
- Matthew R Baird
- Matthew CJ Yip
- Sichen Shao
International Retinal Research Foundation (N/A)
- Alan Brown
E. Matilda Ziegler Foundation for the Blind (N/A)
- Alan Brown
Charles H. Hood Foundation (N/A)
- Sichen Shao
Richard and Susan Smith Family Foundation (N/A)
- Sichen Shao
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Nahum Sonenberg, McGill University, Canada
Publication history
- Received: July 26, 2018
- Accepted: October 12, 2018
- Accepted Manuscript published: October 24, 2018 (version 1)
- Version of Record published: November 9, 2018 (version 2)
Copyright
© 2018, Brown 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.
Metrics
-
- 6,182
- Page views
-
- 928
- Downloads
-
- 37
- Citations
Article citation count generated by polling the highest count across the following sources: Crossref, Scopus, PubMed Central.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Structures of translationally inactive mammalian ribosomes
eLife 7:e40486.
https://doi.org/10.7554/eLife.40486
Further reading
-
- Structural Biology and Molecular Biophysics
We present a new approach for macromolecular structure determination from multiple particles in electron cryo-tomography (cryo-ET) data sets. Whereas existing subtomogram averaging approaches are based on 3D data models, we propose to optimise a regularised likelihood target that approximates a function of the 2D experimental images. In addition, analogous to Bayesian polishing and contrast transfer function (CTF) refinement in single-particle analysis, we describe approaches that exploit the increased signal-to-noise ratio in the averaged structure to optimise tilt series alignments, beam-induced motions of the particles throughout the tilt series acquisition, defoci of the individual particles, as well as higher-order optical aberrations of the microscope. Implementation of our approaches in the open-source software package RELION aims to facilitate their general use, in particular for those researchers who are already familiar with its single-particle analysis tools. We illustrate for three applications that our approaches allow structure determination from cryo-ET data to resolutions sufficient for de novo atomic modelling.
-
- Structural Biology and Molecular Biophysics
Undruggability of RAS proteins has necessitated alternative strategies for the development of effective inhibitors. In this respect, phosphorylation has recently come into prominence as this reversible post-translational modification attenuates sensitivity of RAS towards RAF. As such, in this study, we set out to unveil the impact of phosphorylation on dynamics of HRASWT and aim to invoke similar behavior in HRASG12D mutant by means of small therapeutic molecules. To this end, we performed molecular dynamics (MD) simulations using phosphorylated HRAS and showed that phosphorylation of Y32 distorted Switch I, hence the RAS/RAF interface. Consequently, we targeted Switch I in HRASG12D by means of approved therapeutic molecules and showed that the ligands enabled detachment of Switch I from the nucleotide-binding pocket. Moreover, we demonstrated that displacement of Switch I from the nucleotide-binding pocket was energetically more favorable in the presence of the ligand. Importantly, we verified computational findings in vitro where HRASG12D/RAF interaction was prevented by the ligand in HEK293T cells that expressed HRASG12D mutant protein. Therefore, these findings suggest that targeting Switch I, hence making Y32 accessible might open up new avenues in future drug discovery strategies that target mutant RAS proteins.
