Mechanism of completion of peptidyltransferase centre assembly in eukaryotes
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
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
-
- 3,386
- views
-
- 552
- downloads
-
- 42
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
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)
Further reading
-
- Cell Biology
- Structural Biology and Molecular Biophysics
Acetylation of α-tubulin at the lysine 40 residue (αK40) by αTAT1/MEC-17 acetyltransferase modulates microtubule properties and occurs in most eukaryotic cells. Previous literatures suggest that acetylated microtubules are more stable and damage resistant. αK40 acetylation is the only known microtubule luminal post-translational modification site. The luminal location suggests that the modification tunes the lateral interaction of protofilaments inside the microtubule. In this study, we examined the effect of tubulin acetylation on the doublet microtubule (DMT) in the cilia of Tetrahymena thermophila using a combination of cryo-electron microscopy, molecular dynamics, and mass spectrometry. We found that αK40 acetylation exerts a small-scale effect on the DMT structure and stability by influencing the lateral rotational angle. In addition, comparative mass spectrometry revealed a link between αK40 acetylation and phosphorylation in cilia.
-
- Structural Biology and Molecular Biophysics
The dimeric two-pore OSCA/TMEM63 family has recently been identified as mechanically activated ion channels. Previously, based on the unique features of the structure of OSCA1.2, we postulated the potential involvement of several structural elements in sensing membrane tension (Jojoa-Cruz et al., 2018). Interestingly, while OSCA1, 2, and 3 clades are activated by membrane stretch in cell-attached patches (i.e. they are stretch-activated channels), they differ in their ability to transduce membrane deformation induced by a blunt probe (poking). Here, in an effort to understand the domains contributing to mechanical signal transduction, we used cryo-electron microscopy to solve the structure of Arabidopsis thaliana (At) OSCA3.1, which, unlike AtOSCA1.2, only produced stretch- but not poke-activated currents in our initial characterization (Murthy et al., 2018). Mutagenesis and electrophysiological assessment of conserved and divergent putative mechanosensitive features of OSCA1.2 reveal a selective disruption of the macroscopic currents elicited by poking without considerable effects on stretch-activated currents (SAC). Our results support the involvement of the amphipathic helix and lipid-interacting residues in the membrane fenestration in the response to poking. Our findings position these two structural elements as potential sources of functional diversity within the family.