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
Version 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
-
- 7,603
- views
-
- 1,050
- downloads
-
- 85
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
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
-
- Cell Biology
- Structural Biology and Molecular Biophysics
Mutations in the human PURA gene cause the neurodevelopmental PURA syndrome. In contrast to several other monogenetic disorders, almost all reported mutations in this nucleic acid-binding protein result in the full disease penetrance. In this study, we observed that patient mutations across PURA impair its previously reported co-localization with processing bodies. These mutations either destroyed the folding integrity, RNA binding, or dimerization of PURA. We also solved the crystal structures of the N- and C-terminal PUR domains of human PURA and combined them with molecular dynamics simulations and nuclear magnetic resonance measurements. The observed unusually high dynamics and structural promiscuity of PURA indicated that this protein is particularly susceptible to mutations impairing its structural integrity. It offers an explanation why even conservative mutations across PURA result in the full penetrance of symptoms in patients with PURA syndrome.
-
- Microbiology and Infectious Disease
- Structural Biology and Molecular Biophysics
African trypanosomes replicate within infected mammals where they are exposed to the complement system. This system centres around complement C3, which is present in a soluble form in serum but becomes covalently deposited onto the surfaces of pathogens after proteolytic cleavage to C3b. Membrane-associated C3b triggers different complement-mediated effectors which promote pathogen clearance. To counter complement-mediated clearance, African trypanosomes have a cell surface receptor, ISG65, which binds to C3b and which decreases the rate of trypanosome clearance in an infection model. However, the mechanism by which ISG65 reduces C3b function has not been determined. We reveal through cryogenic electron microscopy that ISG65 has two distinct binding sites for C3b, only one of which is available in C3 and C3d. We show that ISG65 does not block the formation of C3b or the function of the C3 convertase which catalyses the surface deposition of C3b. However, we show that ISG65 forms a specific conjugate with C3b, perhaps acting as a decoy. ISG65 also occludes the binding sites for complement receptors 2 and 3, which may disrupt recruitment of immune cells, including B cells, phagocytes, and granulocytes. This suggests that ISG65 protects trypanosomes by combining multiple approaches to dampen the complement cascade.
