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      The complete structure of the chloroplast 70S ribosome in complex with translation factor pY

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          Abstract

          Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, they still contain their own genome and the machinery for protein biosynthesis. Here, we present the atomic structure of the chloroplast 70S ribosome prepared from spinach leaves and resolved by cryo‐EM at 3.4 Å resolution. The complete structure reveals the features of the 4.5S rRNA, which probably evolved by the fragmentation of the 23S rRNA, and all five plastid‐specific ribosomal proteins. These proteins, required for proper assembly and function of the chloroplast translation machinery, bind and stabilize rRNA including regions that only exist in the chloroplast ribosome. Furthermore, the structure reveals plastid‐specific extensions of ribosomal proteins that extensively remodel the mRNA entry and exit site on the small subunit as well as the polypeptide tunnel exit and the putative binding site of the signal recognition particle on the large subunit. The translation factor pY, involved in light‐ and temperature‐dependent control of protein synthesis, is bound to the mRNA channel of the small subunit and interacts with 16S rRNA nucleotides at the A‐site and P‐site, where it protects the decoding centre and inhibits translation by preventing tRNA binding. The small subunit is locked by pY in a non‐rotated state, in which the intersubunit bridges to the large subunit are stabilized.

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          Improved methods for building protein models in electron density maps and the location of errors in these models.

          Map interpretation remains a critical step in solving the structure of a macromolecule. Errors introduced at this early stage may persist throughout crystallographic refinement and result in an incorrect structure. The normally quoted crystallographic residual is often a poor description for the quality of the model. Strategies and tools are described that help to alleviate this problem. These simplify the model-building process, quantify the goodness of fit of the model on a per-residue basis and locate possible errors in peptide and side-chain conformations.
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            Biogenesis and homeostasis of chloroplasts and other plastids.

            Chloroplasts are the organelles that define plants, and they are responsible for photosynthesis as well as numerous other functions. They are the ancestral members of a family of organelles known as plastids. Plastids are remarkably dynamic, existing in strikingly different forms that interconvert in response to developmental or environmental cues. The genetic system of this organelle and its coordination with the nucleocytosolic system, the import and routing of nucleus-encoded proteins, as well as organellar division all contribute to the biogenesis and homeostasis of plastids. They are controlled by the ubiquitin-proteasome system, which is part of a network of regulatory mechanisms that integrate plastid development into broader programmes of cellular and organismal development.
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              Plastid evolution.

              The ancestors of modern cyanobacteria invented O(2)-generating photosynthesis some 3.6 billion years ago. The conversion of water and CO(2) into energy-rich sugars and O(2) slowly transformed the planet, eventually creating the biosphere as we know it today. Eukaryotes didn't invent photosynthesis; they co-opted it from prokaryotes by engulfing and stably integrating a photoautotrophic prokaryote in a process known as primary endosymbiosis. After approximately a billion of years of coevolution, the eukaryotic host and its endosymbiont have achieved an extraordinary level of integration and have spawned a bewildering array of primary producers that now underpin life on land and in the water. No partnership has been more important to life on earth. Secondary endosymbioses have created additional autotrophic eukaryotic lineages that include key organisms in the marine environment. Some of these organisms have subsequently reverted to heterotrophic lifestyles, becoming significant pathogens, microscopic predators, and consumers. We review the origins, integration, and functions of the different plastid types with special emphasis on their biochemical abilities, transfer of genes to the host, and the back supply of proteins to the endosymbiont.
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                Author and article information

                Contributors
                ban@mol.biol.ethz.ch
                Journal
                EMBO J
                EMBO J
                10.1002/(ISSN)1460-2075
                EMBJ
                embojnl
                The EMBO Journal
                John Wiley and Sons Inc. (Hoboken )
                0261-4189
                1460-2075
                22 December 2016
                15 February 2017
                22 December 2016
                : 36
                : 4 ( doiID: 10.1002/embj.v36.4 )
                : 475-486
                Affiliations
                [ 1 ] Department of Biology Institute of Molecular Biology and Biophysics ETH Zurich Zurich Switzerland
                Author notes
                [*] [* ]Corresponding author. Tel: +41 44 633 27 85; E‐mail: ban@ 123456mol.biol.ethz.ch
                Author information
                http://orcid.org/0000-0002-9527-210X
                Article
                EMBJ201695959
                10.15252/embj.201695959
                5694952
                28007896
                f63bdffd-8faa-40dd-88dd-e841c856ab52
                © 2016 The Authors. Published under the terms of the CC BY NC ND 4.0 license

                This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial‐NoDerivs 4.0 License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.

                History
                : 25 October 2016
                : 24 November 2016
                : 28 November 2016
                Page count
                Figures: 11, Tables: 0, Pages: 12, Words: 9996
                Funding
                Funded by: Swiss National Science Foundation (SNSF)
                Award ID: 310030B_163478
                Award ID: 51NF40_141735_NCCR
                Categories
                Article
                Articles
                Custom metadata
                2.0
                embj201695959
                15 February 2017
                Converter:WILEY_ML3GV2_TO_NLMPMC version:5.2.6 mode:remove_FC converted:20.11.2017

                Molecular biology
                chloroplast,cryo‐em,py,ribosome,translation,plant biology,protein biosynthesis & quality control,structural biology

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