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Smirnova J, Loerke J, Kleinau G, Schmidt A, Bürger J, Meyer EH, Mielke T, Scheerer P, Bock R, Spahn CMT, Zoschke R. Structure of the actively translating plant 80S ribosome at 2.2 Å resolution. Nat Plants 2023; 9:987-1000. [PMID: 37156858 PMCID: PMC10281867 DOI: 10.1038/s41477-023-01407-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/29/2023] [Indexed: 05/10/2023]
Abstract
In plant cells, translation occurs in three compartments: the cytosol, the plastids and the mitochondria. While the structures of the (prokaryotic-type) ribosomes in plastids and mitochondria are well characterized, high-resolution structures of the eukaryotic 80S ribosomes in the cytosol have been lacking. Here the structure of translating tobacco (Nicotiana tabacum) 80S ribosomes was solved by cryo-electron microscopy with a global resolution of 2.2 Å. The ribosome structure includes two tRNAs, decoded mRNA and the nascent peptide chain, thus providing insights into the molecular underpinnings of the cytosolic translation process in plants. The map displays conserved and plant-specific rRNA modifications and the positions of numerous ionic cofactors, and it uncovers the role of monovalent ions in the decoding centre. The model of the plant 80S ribosome enables broad phylogenetic comparisons that reveal commonalities and differences in the ribosomes of plants and those of other eukaryotes, thus putting our knowledge about eukaryotic translation on a firmer footing.
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Affiliation(s)
- Julia Smirnova
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Justus Loerke
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gunnar Kleinau
- Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Andrea Schmidt
- Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jörg Bürger
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Microscopy and Cryo-Electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Etienne H Meyer
- Department III, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Institut für Pflanzenphysiologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Thorsten Mielke
- Microscopy and Cryo-Electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Patrick Scheerer
- Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ralph Bock
- Department III, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
| | - Christian M T Spahn
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Reimo Zoschke
- Department III, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
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2
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Hilal T, Killam BY, Grozdanović M, Dobosz-Bartoszek M, Loerke J, Bürger J, Mielke T, Copeland PR, Simonović M, Spahn CMT. Structure of the mammalian ribosome as it decodes the selenocysteine UGA codon. Science 2022; 376:1338-1343. [PMID: 35709277 PMCID: PMC10064918 DOI: 10.1126/science.abg3875] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The elongation of eukaryotic selenoproteins relies on a poorly understood process of interpreting in-frame UGA stop codons as selenocysteine (Sec). We used cryo-electron microscopy to visualize Sec UGA recoding in mammals. A complex between the noncoding Sec-insertion sequence (SECIS), SECIS-binding protein 2 (SBP2), and 40S ribosomal subunit enables Sec-specific elongation factor eEFSec to deliver Sec. eEFSec and SBP2 do not interact directly but rather deploy their carboxyl-terminal domains to engage with the opposite ends of the SECIS. By using its Lys-rich and carboxyl-terminal segments, the ribosomal protein eS31 simultaneously interacts with Sec-specific transfer RNA (tRNASec) and SBP2, which further stabilizes the assembly. eEFSec is indiscriminate toward l-serine and facilitates its misincorporation at Sec UGA codons. Our results support a fundamentally distinct mechanism of Sec UGA recoding in eukaryotes from that in bacteria.
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Affiliation(s)
- Tarek Hilal
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Benjamin Y. Killam
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Milica Grozdanović
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Malgorzata Dobosz-Bartoszek
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Justus Loerke
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Jörg Bürger
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Max-Planck Institut für Molekulare Genetik, 14195 Berlin, Germany
| | - Thorsten Mielke
- Max-Planck Institut für Molekulare Genetik, 14195 Berlin, Germany
| | - Paul R. Copeland
- Department of Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Miljan Simonović
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Christian M. T. Spahn
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
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3
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Nikolay R, Hilal T, Schmidt S, Qin B, Schwefel D, Vieira-Vieira CH, Mielke T, Bürger J, Loerke J, Amikura K, Flügel T, Ueda T, Selbach M, Deuerling E, Spahn CMT. Snapshots of native pre-50S ribosomes reveal a biogenesis factor network and evolutionary specialization. Mol Cell 2021; 81:1200-1215.e9. [PMID: 33639093 DOI: 10.1016/j.molcel.2021.02.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 11/11/2020] [Accepted: 02/02/2021] [Indexed: 01/13/2023]
Abstract
Ribosome biogenesis is a fundamental multi-step cellular process that culminates in the formation of ribosomal subunits, whose production and modification are regulated by numerous biogenesis factors. In this study, we analyze physiologic prokaryotic ribosome biogenesis by isolating bona fide pre-50S subunits from an Escherichia coli strain with the biogenesis factor ObgE, affinity tagged at its native gene locus. Our integrative structural approach reveals a network of interacting biogenesis factors consisting of YjgA, RluD, RsfS, and ObgE on the immature pre-50S subunit. In addition, our study provides mechanistic insight into how the GTPase ObgE, in concert with other biogenesis factors, facilitates the maturation of the 50S functional core and reveals both conserved and divergent evolutionary features of ribosome biogenesis between prokaryotes and eukaryotes.
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Affiliation(s)
- Rainer Nikolay
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
| | - Tarek Hilal
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Freie Universität Berlin, Research Centre for Electron Microscopy, Fabeckstr. 36a, 14195 Berlin, Germany
| | - Sabine Schmidt
- Molekulare Mikrobiologie, Universität Konstanz, Konstanz, Germany
| | - Bo Qin
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - David Schwefel
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Carlos H Vieira-Vieira
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany; Faculty of Life Sciences, Humboldt Universität zu Berlin, Berlin, Germany
| | - Thorsten Mielke
- Microscopy and Cryo-Electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Jörg Bürger
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Microscopy and Cryo-Electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Justus Loerke
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Kazuaki Amikura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, FSB-401, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Timo Flügel
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Takuya Ueda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, FSB-401, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany; Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Elke Deuerling
- Molekulare Mikrobiologie, Universität Konstanz, Konstanz, Germany
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
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4
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Liu P, Zupa E, Neuner A, Böhler A, Loerke J, Flemming D, Ruppert T, Rudack T, Peter C, Spahn C, Gruss OJ, Pfeffer S, Schiebel E. Insights into the assembly and activation of the microtubule nucleator γ-TuRC. Nature 2019; 578:467-471. [DOI: 10.1038/s41586-019-1896-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/10/2019] [Indexed: 02/06/2023]
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5
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Flis J, Holm M, Rundlet EJ, Loerke J, Hilal T, Dabrowski M, Bürger J, Mielke T, Blanchard SC, Spahn CMT, Budkevich TV. tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis. Cell Rep 2018; 25:2676-2688.e7. [PMID: 30517857 PMCID: PMC6314685 DOI: 10.1016/j.celrep.2018.11.040] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 09/14/2018] [Accepted: 11/09/2018] [Indexed: 01/04/2023] Open
Abstract
Translocation moves the tRNA2⋅mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes within both the ribosome and tRNA substrates, the orchestrated events that ensure the speed and fidelity of this critical aspect of the protein synthesis mechanism have not been fully elucidated. Here, we present three high-resolution structures of intermediates of translocation on the mammalian ribosome where, in contrast to bacteria, ribosomal complexes containing the translocase eEF2 and the complete tRNA2⋅mRNA module are trapped by the non-hydrolyzable GTP analog GMPPNP. Consistent with the observed structures, single-molecule imaging revealed that GTP hydrolysis principally facilitates rate-limiting, final steps of translocation, which are required for factor dissociation and which are differentially regulated in bacterial and mammalian systems by the rates of deacyl-tRNA dissociation from the E site.
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Affiliation(s)
- Julia Flis
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Mikael Holm
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Emily J Rundlet
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, New York, NY, USA
| | - Justus Loerke
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Tarek Hilal
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Marylena Dabrowski
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Jörg Bürger
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Thorsten Mielke
- UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, New York, NY, USA.
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Tatyana V Budkevich
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
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6
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Qureshi BM, Behrmann E, Schöneberg J, Loerke J, Bürger J, Mielke T, Giesebrecht J, Noé F, Lamb TD, Hofmann KP, Spahn CMT, Heck M. It takes two transducins to activate the cGMP-phosphodiesterase 6 in retinal rods. Open Biol 2018; 8:180075. [PMID: 30068566 PMCID: PMC6119865 DOI: 10.1098/rsob.180075] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 07/06/2018] [Indexed: 12/21/2022] Open
Abstract
Among cyclic nucleotide phosphodiesterases (PDEs), PDE6 is unique in serving as an effector enzyme in G protein-coupled signal transduction. In retinal rods and cones, PDE6 is membrane-bound and activated to hydrolyse its substrate, cGMP, by binding of two active G protein α-subunits (Gα*). To investigate the activation mechanism of mammalian rod PDE6, we have collected functional and structural data, and analysed them by reaction-diffusion simulations. Gα* titration of membrane-bound PDE6 reveals a strong functional asymmetry of the enzyme with respect to the affinity of Gα* for its two binding sites on membrane-bound PDE6 and the enzymatic activity of the intermediary 1 : 1 Gα* · PDE6 complex. Employing cGMP and its 8-bromo analogue as substrates, we find that Gα* · PDE6 forms with high affinity but has virtually no cGMP hydrolytic activity. To fully activate PDE6, it takes a second copy of Gα* which binds with lower affinity, forming Gα* · PDE6 · Gα*. Reaction-diffusion simulations show that the functional asymmetry of membrane-bound PDE6 constitutes a coincidence switch and explains the lack of G protein-related noise in visual signal transduction. The high local concentration of Gα* generated by a light-activated rhodopsin molecule efficiently activates PDE6, whereas the low density of spontaneously activated Gα* fails to activate the effector enzyme.
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Affiliation(s)
- Bilal M Qureshi
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Elmar Behrmann
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Johannes Schöneberg
- Department of Mathematics, Computer Science and Bioinformatics, Freie Universität Berlin, Berlin, Germany
| | - Justus Loerke
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jörg Bürger
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Thorsten Mielke
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Microscopy and Cryo Electron Microscopy Group, Max-Planck Institut für Molekulare Genetik, Berlin, Germany
| | - Jan Giesebrecht
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Frank Noé
- Department of Mathematics, Computer Science and Bioinformatics, Freie Universität Berlin, Berlin, Germany
| | - Trevor D Lamb
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 2600, Australia
| | - Klaus Peter Hofmann
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Zentrum für Biophysik und Bioinformatik, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Martin Heck
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
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7
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Said N, Krupp F, Anedchenko E, Santos KF, Dybkov O, Huang YH, Lee CT, Loll B, Behrmann E, Bürger J, Mielke T, Loerke J, Urlaub H, Spahn CMT, Weber G, Wahl MC. Structural basis for λN-dependent processive transcription antitermination. Nat Microbiol 2017; 2:17062. [DOI: 10.1038/nmicrobiol.2017.62] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/24/2017] [Indexed: 11/09/2022]
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8
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Hilal T, Yamamoto H, Loerke J, Bürger J, Mielke T, Spahn CM. Structural insights into ribosomal rescue by Dom34 and Hbs1 at near-atomic resolution. Nat Commun 2016; 7:13521. [PMID: 27995908 PMCID: PMC5187420 DOI: 10.1038/ncomms13521] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/11/2016] [Indexed: 01/13/2023] Open
Abstract
The surveillance of mRNA translation is imperative for homeostasis. Monitoring the integrity of the message is essential, as the translation of aberrant mRNAs leads to stalling of the translational machinery. During ribosomal rescue, arrested ribosomes are specifically recognized by the conserved eukaryotic proteins Dom34 and Hbs1, to initiate their recycling. Here we solve the structure of Dom34 and Hbs1 bound to a yeast ribosome programmed with a nonstop mRNA at 3.3 Å resolution using cryo-electron microscopy. The structure shows that Domain N of Dom34 is inserted into the upstream mRNA-binding groove via direct stacking interactions with conserved nucleotides of 18S rRNA. It senses the absence of mRNA at the A-site and part of the mRNA entry channel by direct competition. Thus, our analysis establishes the structural foundation for the recognition of aberrantly stalled 80S ribosomes by the Dom34·Hbs1·GTP complex during Dom34-mediated mRNA surveillance pathways.
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Affiliation(s)
- Tarek Hilal
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Hiroshi Yamamoto
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Justus Loerke
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Jörg Bürger
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- Max-Planck Institut für Molekulare Genetik, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Thorsten Mielke
- Max-Planck Institut für Molekulare Genetik, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Christian M.T. Spahn
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
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9
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Sprink T, Ramrath DJF, Yamamoto H, Yamamoto K, Loerke J, Ismer J, Hildebrand PW, Scheerer P, Bürger J, Mielke T, Spahn CMT. Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association. Sci Adv 2016; 2:e1501502. [PMID: 26973877 PMCID: PMC4783127 DOI: 10.1126/sciadv.1501502] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 01/12/2016] [Indexed: 05/30/2023]
Abstract
Throughout the four phases of protein biosynthesis-initiation, elongation, termination, and recycling-the ribosome is controlled and regulated by at least one specified translational guanosine triphosphatase (trGTPase). Although the structural basis for trGTPase interaction with the ribosome has been solved for the last three steps of translation, the high-resolution structure for the key initiation trGTPase, initiation factor 2 (IF2), complexed with the ribosome, remains elusive. We determine the structure of IF2 complexed with a nonhydrolyzable guanosine triphosphate analog and initiator fMet-tRNAi (Met) in the context of the Escherichia coli ribosome to 3.7-Å resolution using cryo-electron microscopy. The structural analysis reveals previously unseen intrinsic conformational modes of the 70S initiation complex, establishing the mutual interplay of IF2 and initator transfer RNA (tRNA) with the ribsosome and providing the structural foundation for a mechanistic understanding of the final steps of translation initiation.
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Affiliation(s)
- Thiemo Sprink
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - David J F Ramrath
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Hiroshi Yamamoto
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Kaori Yamamoto
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Justus Loerke
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Jochen Ismer
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Peter W Hildebrand
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Patrick Scheerer
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Jörg Bürger
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.; UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Thorsten Mielke
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.; UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
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10
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Yamamoto H, Collier M, Loerke J, Ismer J, Schmidt A, Hilal T, Sprink T, Yamamoto K, Mielke T, Bürger J, Shaikh TR, Dabrowski M, Hildebrand PW, Scheerer P, Spahn CMT. Molecular architecture of the ribosome-bound Hepatitis C Virus internal ribosomal entry site RNA. EMBO J 2015; 34:3042-58. [PMID: 26604301 DOI: 10.15252/embj.201592469] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 10/29/2015] [Indexed: 12/12/2022] Open
Abstract
Internal ribosomal entry sites (IRESs) are structured cis-acting RNAs that drive an alternative, cap-independent translation initiation pathway. They are used by many viruses to hijack the translational machinery of the host cell. IRESs facilitate translation initiation by recruiting and actively manipulating the eukaryotic ribosome using only a subset of canonical initiation factor and IRES transacting factors. Here we present cryo-EM reconstructions of the ribosome 80S- and 40S-bound Hepatitis C Virus (HCV) IRES. The presence of four subpopulations for the 80S•HCV IRES complex reveals dynamic conformational modes of the complex. At a global resolution of 3.9 Å for the most stable complex, a derived atomic model reveals a complex fold of the IRES RNA and molecular details of its interaction with the ribosome. The comparison of obtained structures explains how a modular architecture facilitates mRNA loading and tRNA binding to the P-site. This information provides the structural foundation for understanding the mechanism of HCV IRES RNA-driven translation initiation.
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Affiliation(s)
- Hiroshi Yamamoto
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany
| | - Marianne Collier
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany
| | - Justus Loerke
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany
| | - Jochen Ismer
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany
| | - Andrea Schmidt
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany
| | - Tarek Hilal
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany
| | - Thiemo Sprink
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany
| | - Kaori Yamamoto
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany
| | - Thorsten Mielke
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Jörg Bürger
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Tanvir R Shaikh
- Structural Biology Programme, CEITEC, Masaryk University, Brno, Czech Republic
| | - Marylena Dabrowski
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany
| | - Peter W Hildebrand
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany
| | - Patrick Scheerer
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin, Berlin, Germany
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11
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Qureshi BM, Behrmann E, Schöneberg J, Loerke J, Bürger J, Mielke T, Giesebrecht J, Noé F, Hofmann KP, Spahn CMT, Heck M. Asymmetric properties of rod cGMP Phosphodiesterase 6 (PDE6): structural and functional analysis. BMC Pharmacol Toxicol 2015. [PMCID: PMC4565112 DOI: 10.1186/2050-6511-16-s1-a76] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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12
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Kirmizialtin S, Loerke J, Behrmann E, Spahn CMT, Sanbonmatsu KY. Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions. Methods Enzymol 2015; 558:497-514. [PMID: 26068751 DOI: 10.1016/bs.mie.2015.02.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
An explosion of new data from high-resolution cryo-electron microscopy (cryo-EM) studies has produced a large number of data sets for many species of ribosomes in various functional states over the past few years. While many methods exist to produce structural models for lower resolution cryo-EM reconstructions, high-resolution reconstructions are often modeled using crystallographic techniques and extensive manual intervention. Here, we present an automated fitting technique for high-resolution cryo-EM data sets that produces all-atom models highly consistent with the EM density. Using a molecular dynamics approach, atomic positions are optimized with a potential that includes the cross-correlation coefficient between the structural model and the cryo-EM electron density, as well as a biasing potential preserving the stereochemistry and secondary structure of the biomolecule. Specifically, we use a hybrid structure-based/ab initio molecular dynamics potential to extend molecular dynamics fitting. In addition, we find that simulated annealing integration, as opposed to straightforward molecular dynamics integration, significantly improves performance. We obtain atomistic models of the human ribosome consistent with high-resolution cryo-EM reconstructions of the human ribosome. Automated methods such as these have the potential to produce atomistic models for a large number of ribosome complexes simultaneously that can be subsequently refined manually.
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Affiliation(s)
- Serdal Kirmizialtin
- Department of Chemistry, New York University, Abu Dhabi, United Arab Emirates; New Mexico Consortium, Los Alamos, New Mexico, USA; Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Justus Loerke
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Elmar Behrmann
- Structural Dynamics of Proteins, Center of Advanced European Studies and Research (CAESAR), Bonn, Germany
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Karissa Y Sanbonmatsu
- New Mexico Consortium, Los Alamos, New Mexico, USA; Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.
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13
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Behrmann E, Loerke J, Budkevich TV, Yamamoto K, Schmidt A, Penczek PA, Vos MR, Bürger J, Mielke T, Scheerer P, Spahn CMT. Structural snapshots of actively translating human ribosomes. Cell 2015; 161:845-57. [PMID: 25957688 PMCID: PMC4432480 DOI: 10.1016/j.cell.2015.03.052] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 01/05/2015] [Accepted: 02/27/2015] [Indexed: 10/23/2022]
Abstract
Macromolecular machines, such as the ribosome, undergo large-scale conformational changes during their functional cycles. Although their mode of action is often compared to that of mechanical machines, a crucial difference is that, at the molecular dimension, thermodynamic effects dominate functional cycles, with proteins fluctuating stochastically between functional states defined by energetic minima on an energy landscape. Here, we have used cryo-electron microscopy to image ex-vivo-derived human polysomes as a source of actively translating ribosomes. Multiparticle refinement and 3D variability analysis allowed us to visualize a variety of native translation intermediates. Significantly populated states include not only elongation cycle intermediates in pre- and post-translocational states, but also eEF1A-containing decoding and termination/recycling complexes. Focusing on the post-translocational state, we extended this assessment to the single-residue level, uncovering striking details of ribosome-ligand interactions and identifying both static and functionally important dynamic elements.
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Affiliation(s)
- Elmar Behrmann
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Justus Loerke
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Tatyana V Budkevich
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Kaori Yamamoto
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Andrea Schmidt
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; Institut für Medizinische Physik und Biophysik, AG Protein X-Ray Crystallography, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Pawel A Penczek
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School, 6431 Fannin MSB 6.220, Houston, TX 77054, USA
| | - Matthijn R Vos
- FEI Company, Nanoport Europe, Achtseweg Noord 5, 5651 GG Eindhoven, the Netherlands
| | - Jörg Bürger
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Thorsten Mielke
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; Max-Planck Institut für Molekulare Genetik, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Patrick Scheerer
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; Institut für Medizinische Physik und Biophysik, AG Protein X-Ray Crystallography, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
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14
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Budkevich TV, Giesebrecht J, Behrmann E, Loerke J, Ramrath DJF, Mielke T, Ismer J, Hildebrand PW, Tung CS, Nierhaus KH, Sanbonmatsu KY, Spahn CMT. Regulation of the mammalian elongation cycle by subunit rolling: a eukaryotic-specific ribosome rearrangement. Cell 2014; 158:121-31. [PMID: 24995983 DOI: 10.1016/j.cell.2014.04.044] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 02/24/2014] [Accepted: 04/18/2014] [Indexed: 11/15/2022]
Abstract
The extent to which bacterial ribosomes and the significantly larger eukaryotic ribosomes share the same mechanisms of ribosomal elongation is unknown. Here, we present subnanometer resolution cryoelectron microscopy maps of the mammalian 80S ribosome in the posttranslocational state and in complex with the eukaryotic eEF1A⋅Val-tRNA⋅GMPPNP ternary complex, revealing significant differences in the elongation mechanism between bacteria and mammals. Surprisingly, and in contrast to bacterial ribosomes, a rotation of the small subunit around its long axis and orthogonal to the well-known intersubunit rotation distinguishes the posttranslocational state from the classical pretranslocational state ribosome. We term this motion "subunit rolling." Correspondingly, a mammalian decoding complex visualized in substates before and after codon recognition reveals structural distinctions from the bacterial system. These findings suggest how codon recognition leads to GTPase activation in the mammalian system and demonstrate that in mammalia subunit rolling occurs during tRNA selection.
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Affiliation(s)
- Tatyana V Budkevich
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; Max-Planck Institut für Molekulare Genetik, Abteilung Vingron, AG Ribosomen, 14195 Berlin, Ihnestraße 73, Germany; Institute of Molecular Biology and Genetics, Group of Protein Biosynthesis, 03143 Kiev, Ukraine
| | - Jan Giesebrecht
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Elmar Behrmann
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Justus Loerke
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - David J F Ramrath
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Thorsten Mielke
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; Max-Planck Institut für Molekulare Genetik, UltraStrukturNetzwerk, 14195 Berlin, Ihnestraße 73, Germany
| | - Jochen Ismer
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Peter W Hildebrand
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Chang-Shung Tung
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, MK710, Los Alamos, NM 87545, USA
| | - Knud H Nierhaus
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; Max-Planck Institut für Molekulare Genetik, Abteilung Vingron, AG Ribosomen, 14195 Berlin, Ihnestraße 73, Germany
| | - Karissa Y Sanbonmatsu
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, MK710, Los Alamos, NM 87545, USA; New Mexico Consortium, 4200 West Jemez Road, Suite 301, Los Alamos, New Mexico 87544, USA
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
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15
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Penczek PA, Fang J, Li X, Cheng Y, Loerke J, Spahn CMT. CTER-rapid estimation of CTF parameters with error assessment. Ultramicroscopy 2014; 140:9-19. [PMID: 24562077 DOI: 10.1016/j.ultramic.2014.01.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 01/22/2014] [Accepted: 01/27/2014] [Indexed: 10/25/2022]
Abstract
In structural electron microscopy, the accurate estimation of the Contrast Transfer Function (CTF) parameters, particularly defocus and astigmatism, is of utmost importance for both initial evaluation of micrograph quality and for subsequent structure determination. Due to increases in the rate of data collection on modern microscopes equipped with new generation cameras, it is also important that the CTF estimation can be done rapidly and with minimal user intervention. Finally, in order to minimize the necessity for manual screening of the micrographs by a user it is necessary to provide an assessment of the errors of fitted parameters values. In this work we introduce CTER, a CTF parameters estimation method distinguished by its computational efficiency. The efficiency of the method makes it suitable for high-throughput EM data collection, and enables the use of a statistical resampling technique, bootstrap, that yields standard deviations of estimated defocus and astigmatism amplitude and angle, thus facilitating the automation of the process of screening out inferior micrograph data. Furthermore, CTER also outputs the spatial frequency limit imposed by reciprocal space aliasing of the discrete form of the CTF and the finite window size. We demonstrate the efficiency and accuracy of CTER using a data set collected on a 300kV Tecnai Polara (FEI) using the K2 Summit DED camera in super-resolution counting mode. Using CTER we obtained a structure of the 80S ribosome whose large subunit had a resolution of 4.03Å without, and 3.85Å with, inclusion of astigmatism parameters.
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Affiliation(s)
- Pawel A Penczek
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School, 6431 Fannin MSB 6.220, Houston, TX 77054, USA.
| | - Jia Fang
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School, 6431 Fannin MSB 6.220, Houston, TX 77054, USA
| | - Xueming Li
- The Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Yifan Cheng
- The Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Justus Loerke
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
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16
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Ratje AH, Loerke J, Mikolajka A, Brünner M, Hildebrand PW, Starosta AL, Dönhöfer A, Connell SR, Fucini P, Mielke T, Whitford PC, Onuchic JN, Yu Y, Sanbonmatsu KY, Hartmann RK, Penczek PA, Wilson DN, Spahn CMT. Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites. Nature 2011; 468:713-6. [PMID: 21124459 PMCID: PMC3272701 DOI: 10.1038/nature09547] [Citation(s) in RCA: 287] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Accepted: 09/30/2010] [Indexed: 11/09/2022]
Abstract
The elongation cycle of protein synthesis involves the delivery of aminoacyl-transfer RNAs to the aminoacyl-tRNA-binding site (A site) of the ribosome, followed by peptide-bond formation and translocation of the tRNAs through the ribosome to reopen the A site. The translocation reaction is catalysed by elongation factor G (EF-G) in a GTP-dependent manner. Despite the availability of structures of various EF-G-ribosome complexes, the precise mechanism by which tRNAs move through the ribosome still remains unclear. Here we use multiparticle cryoelectron microscopy analysis to resolve two previously unseen subpopulations within Thermus thermophilus EF-G-ribosome complexes at subnanometre resolution, one of them with a partly translocated tRNA. Comparison of these substates reveals that translocation of tRNA on the 30S subunit parallels the swivelling of the 30S head and is coupled to unratcheting of the 30S body. Because the tRNA maintains contact with the peptidyl-tRNA-binding site (P site) on the 30S head and simultaneously establishes interaction with the exit site (E site) on the 30S platform, a novel intra-subunit 'pe/E' hybrid state is formed. This state is stabilized by domain IV of EF-G, which interacts with the swivelled 30S-head conformation. These findings provide direct structural and mechanistic insight into the 'missing link' in terms of tRNA intermediates involved in the universally conserved translocation process.
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Affiliation(s)
- Andreas H Ratje
- Institut für Medizinische Physik und Biophysik, Charite - Universitätsmedizin Berlin, Ziegelstrasse 5-9, 10117-Berlin, Germany
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17
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Abstract
As the resolution of cryo-EM reconstructions has improved to the subnanometer range, conformational and compositional heterogeneity have become increasing problems in cryo-EM, limiting the resolution of reconstructions. Since further purification is not feasible, the presence of several conformational states of ribosomal complexes in thermodynamic equilibrium requires methods for separating these states in silico. We describe a procedure for generating subnanometer resolution cryo-EM structures from large sets of projection images of ribosomal complexes. The incremental K-means-like method of unsupervised 3D sorting discussed here allows separation of classes in the dataset by exploiting intrinsic divisions in the data. The classification procedure is described in detail and its effectiveness is illustrated using current examples from our work. Through a good separation of conformational modes, higher resolution reconstructions can be calculated. This increases information gained from single states, while exploiting the coexistence of multiple states to gather comprehensive mechanistic insight into biological processes like ribosomal translocation.
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Affiliation(s)
- Justus Loerke
- Institut für medizinische Physik und Biophysik, Charité, Universitätsmedizin Berlin, Berlin, Germany
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18
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Schuette JC, Murphy FV, Kelley AC, Weir JR, Giesebrecht J, Connell SR, Loerke J, Mielke T, Zhang W, Penczek PA, Ramakrishnan V, Spahn CMT. GTPase activation of elongation factor EF-Tu by the ribosome during decoding. EMBO J 2009; 28:755-65. [PMID: 19229291 PMCID: PMC2666022 DOI: 10.1038/emboj.2009.26] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Accepted: 01/14/2009] [Indexed: 11/09/2022] Open
Abstract
We have used single-particle reconstruction in cryo-electron microscopy to determine a structure of the Thermus thermophilus ribosome in which the ternary complex of elongation factor Tu (EF-Tu), tRNA and guanine nucleotide has been trapped on the ribosome using the antibiotic kirromycin. This represents the state in the decoding process just after codon recognition by tRNA and the resulting GTP hydrolysis by EF-Tu, but before the release of EF-Tu from the ribosome. Progress in sample purification and image processing made it possible to reach a resolution of 6.4 A. Secondary structure elements in tRNA, EF-Tu and the ribosome, and even GDP and kirromycin, could all be visualized directly. The structure reveals a complex conformational rearrangement of the tRNA in the A/T state and the interactions with the functionally important switch regions of EF-Tu crucial to GTP hydrolysis. Thus, the structure provides insights into the molecular mechanism of signalling codon recognition from the decoding centre of the 30S subunit to the GTPase centre of EF-Tu.
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Affiliation(s)
- Jan-Christian Schuette
- Institut für Medizinische Physik und Biophysik, Charite-Universitätsmedizin Berlin, Berlin, Germany
| | - Frank V Murphy
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Ann C Kelley
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - John R Weir
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Jan Giesebrecht
- Institut für Medizinische Physik und Biophysik, Charite-Universitätsmedizin Berlin, Berlin, Germany
| | - Sean R Connell
- Institut für Medizinische Physik und Biophysik, Charite-Universitätsmedizin Berlin, Berlin, Germany
| | - Justus Loerke
- UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Thorsten Mielke
- UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Wei Zhang
- Department of Biochemistry and Molecular Biology, The University of Texas—Houston Medical School, Houston, TX, USA
| | - Pawel A Penczek
- Department of Biochemistry and Molecular Biology, The University of Texas—Houston Medical School, Houston, TX, USA
| | - V Ramakrishnan
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charite-Universitätsmedizin Berlin, Berlin, Germany
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Bordo VG, Loerke J, Rubahn HG. Two-photon evanescent-volume wave spectroscopy: a new account of gas-solid dynamics in the boundary layer. Phys Rev Lett 2001; 86:1490-1493. [PMID: 11290175 DOI: 10.1103/physrevlett.86.1490] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2000] [Indexed: 05/23/2023]
Abstract
A novel type of laser spectroscopy for the investigation of the collisional dynamics of atoms in the close vicinity of a surface has been developed. The technique utilizes excitation of the vapor atoms in two crossed laser fields, one of which is directed normally to the surface, whereas the other one excites an evanescent wave propagating along the surface. The results, obtained for sodium atoms near a dielectric prism surface, are quantitatively reproduced by a rigorous theoretical approach. This new, nonintrusive method allows one to distinguish by pure optical means between different groups of atoms and to extract their two-dimensional velocity distributions.
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Affiliation(s)
- V G Bordo
- Fysisk Institut, Odense Universitet, Denmark
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