Mechanism of completion of peptidyltransferase centre assembly in eukaryotes
- Cambridge Institute for Medical Research, United Kingdom
- University of Konstanz, Germany
- University of Graz, Austria
- MRC Laboratory of Molecular Biology, United Kingdom
- University of Leeds, United Kingdom
Abstract
During their final maturation in the cytoplasm, pre-60S ribosomal particles are converted to translation-competent large ribosomal subunits. Here, we present the mechanism of peptidyltransferase centre (PTC) completion that explains how integration of the last ribosomal proteins is coupled to release of the nuclear export adaptor Nmd3. Single-particle cryo-EM reveals that eL40 recruitment stabilizes helix 89 to form the uL16 binding site. The loading of uL16 unhooks helix 38 from Nmd3 to adopt its mature conformation. In turn, partial retraction of the L1 stalk is coupled to a conformational switch in Nmd3 that allows the uL16 P-site loop to fully accommodate into the PTC where it competes with Nmd3 for an overlapping binding site (base A2971). Our data reveal how the central functional site of the ribosome is sculpted and suggest how the formation of translation-competent 60S subunits is disrupted in leukaemia-associated ribosomopathies.
Data availability
The cryo-EM density maps have been deposited in the Electron Microscopy Data Bank with accession numbers EMD-4558, EMD-4559, EMD-4560, EMD-4636, EMD-4884 and EMD-4630. Atomic coordinates have been deposited in the Protein Data Bank, with entry codes 6QIF, 6QIJ, 6QIK, 6QTZ, 6RI5 and 6QT0.
-
Atomic model of cytoplasmic 60S ribosomal subunit (state I)Protein Data Bank, 6QIF.
-
Atomic model of cytoplasmic 60S ribosomal subunit (state I)Protein Data Bank, 6QIJ.
-
Atomic model of cytoplasmic 60S ribosomal subunit (state I)Protein Data Bank, 6QIK.
-
Atomic model of cytoplasmic 60S ribosomal subunit (state I)Protein Data Bank, 6QTZ.
-
Atomic model of cytoplasmic 60S ribosomal subunit (state I)Protein Data Bank, 6RI5.
-
Atomic model of cytoplasmic 60S ribosomal subunit (state I)Protein Data Bank, 6QT0.
Article and author information
Author details
Norberto Escudero-Urquijo
Funding
Medical Research Council (MC_U105161083)
- Alan John Warren
Bloodwise (12048)
- Alan John Warren
Wellcome (108466/Z/15/Z)
- Edwin Chen
German Science Foundation Emmy Noether Foundation (STE 2517/1-1)
- Florian Stengel
Collaborative Research Center (969 Project A06)
- Florian Stengel
Austrian Science Foundation FWF Grants (P26136)
- Helmut Bergler
Austrian Science Foundation FWF Grants (P29451)
- Helmut Bergler
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: January 5, 2019
- Accepted: May 20, 2019
- Accepted Manuscript published: May 22, 2019 (version 1)
- Version of Record published: June 17, 2019 (version 2)
Copyright
© 2019, Kargas 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
-
- 3,438
- views
-
- 556
- downloads
-
- 50
- 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)
Mechanism of completion of peptidyltransferase centre assembly in eukaryotes
eLife 8:e44904.
https://doi.org/10.7554/eLife.44904
Further reading
-
- Microbiology and Infectious Disease
- Structural Biology and Molecular Biophysics
Genetic diversity is a hallmark of RNA viruses and the basis for their evolutionary success. Taking advantage of the uniquely large genomic database of SARS-CoV-2, we examine the impact of mutations across the spectrum of viable amino acid sequences on the biophysical phenotypes of the highly expressed and multifunctional nucleocapsid protein. We find variation in the physicochemical parameters of its extended intrinsically disordered regions (IDRs) sufficient to allow local plasticity, but also observe functional constraints that similarly occur in related coronaviruses. In biophysical experiments with several N-protein species carrying mutations associated with major variants, we find that point mutations in the IDRs can have nonlocal impact and modulate thermodynamic stability, secondary structure, protein oligomeric state, particle formation, and liquid-liquid phase separation. In the Omicron variant, distant mutations in different IDRs have compensatory effects in shifting a delicate balance of interactions controlling protein assembly properties, and include the creation of a new protein-protein interaction interface in the N-terminal IDR through the defining P13L mutation. A picture emerges where genetic diversity is accompanied by significant variation in biophysical characteristics of functional N-protein species, in particular in the IDRs.
-
- Microbiology and Infectious Disease
- Structural Biology and Molecular Biophysics
A new study reveals how naturally occurring mutations affect the biophysical properties of nucleocapsid proteins in SARS-CoV-2.
