{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T09:13:18Z","timestamp":1790500398612,"version":"4.1.0"},"reference-count":79,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2019,7,12]],"date-time":"2019-07-12T00:00:00Z","timestamp":1562889600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001837","name":"Estonian Science Foundation","doi-asserted-by":"publisher","award":["PRG335"],"award-info":[{"award-number":["PRG335"]}],"id":[{"id":"10.13039\/501100001837","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","award":["2017-03783"],"award-info":[{"award-number":["2017-03783"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","award":["2015-04746"],"award-info":[{"award-number":["2015-04746"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","award":["2017-04663"],"award-info":[{"award-number":["2017-04663"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007459","name":"Ragnar S\u00f6derberg foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007459","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007067","name":"Kempestiftelsernas","doi-asserted-by":"publisher","award":["JCK-1627"],"award-info":[{"award-number":["JCK-1627"]}],"id":[{"id":"10.13039\/501100007067","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007067","name":"Kempestiftelsernas","doi-asserted-by":"publisher","award":["SMK-1349"],"award-info":[{"award-number":["SMK-1349"]}],"id":[{"id":"10.13039\/501100007067","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006285","name":"Magnus Bergvalls Foundation","doi-asserted-by":"publisher","award":["2017-02098"],"award-info":[{"award-number":["2017-02098"]}],"id":[{"id":"10.13039\/501100006285","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007435","name":"\u00c5ke Wibergs Foundation","doi-asserted-by":"publisher","award":["M14-0207"],"award-info":[{"award-number":["M14-0207"]}],"id":[{"id":"10.13039\/100007435","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["WI3285\/8-1"],"award-info":[{"award-number":["WI3285\/8-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010661","name":"Horizon 2020","doi-asserted-by":"publisher","award":["2643"],"award-info":[{"award-number":["2643"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003335","name":"MEYS","doi-asserted-by":"publisher","award":["LM2015043"],"award-info":[{"award-number":["LM2015043"]}],"id":[{"id":"10.13039\/501100003335","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,19]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Translation is controlled by numerous accessory proteins and translation factors. In the yeast Saccharomyces cerevisiae, translation elongation requires an essential elongation factor, the ABCF ATPase eEF3. A closely related protein, New1, is encoded by a non-essential gene with cold sensitivity and ribosome assembly defect knock-out phenotypes. Since the exact molecular function of New1 is unknown, it is unclear if the ribosome assembly defect is direct, i.e. New1 is a bona fide assembly factor, or indirect, for instance due to a defect in protein synthesis. To investigate this, we employed yeast genetics, cryo-electron microscopy (cryo-EM) and ribosome profiling (Ribo-Seq) to interrogate the molecular function of New1. Overexpression of New1 rescues the inviability of a yeast strain lacking the otherwise strictly essential translation factor eEF3. The structure of the ATPase-deficient (EQ2) New1 mutant locked on the 80S ribosome reveals that New1 binds analogously to the ribosome as eEF3. Finally, Ribo-Seq analysis revealed that loss of New1 leads to ribosome queuing upstream of 3\u2032-terminal lysine and arginine codons, including those genes encoding proteins of the cytoplasmic translational machinery. Our results suggest that New1 is a translation factor that fine-tunes the efficiency of translation termination or ribosome recycling.<\/jats:p>","DOI":"10.1093\/nar\/gkz600","type":"journal-article","created":{"date-parts":[[2019,7,11]],"date-time":"2019-07-11T19:10:41Z","timestamp":1562872241000},"page":"8807-8820","source":"Crossref","is-referenced-by-count":39,"title":["A role for the Saccharomyces cerevisiae ABCF protein New1 in translation termination\/recycling"],"prefix":"10.1093","volume":"47","author":[{"given":"Villu","family":"Kasari","sequence":"first","affiliation":[{"name":"Department of Molecular Biology, Ume\u00e5 University, Building 6K, 6L University Hospital Area, 90187 Ume\u00e5, Sweden"},{"name":"Laboratory for Molecular Infection Medicine Sweden (MIMS), Ume\u00e5 University, Building 6K and 6L, University Hospital Area, 90187 Ume\u00e5, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Agnieszka A","family":"Pochopien","sequence":"additional","affiliation":[{"name":"Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"T\u00f5nu","family":"Margus","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, Ume\u00e5 University, Building 6K, 6L University Hospital Area, 90187 Ume\u00e5, Sweden"},{"name":"Laboratory for Molecular Infection Medicine Sweden (MIMS), Ume\u00e5 University, Building 6K and 6L, University Hospital Area, 90187 Ume\u00e5, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victoriia","family":"Murina","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, Ume\u00e5 University, Building 6K, 6L University Hospital Area, 90187 Ume\u00e5, Sweden"},{"name":"Laboratory for Molecular Infection Medicine Sweden (MIMS), Ume\u00e5 University, Building 6K and 6L, University Hospital Area, 90187 Ume\u00e5, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathryn","family":"Turnbull","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, Ume\u00e5 University, Building 6K, 6L University Hospital Area, 90187 Ume\u00e5, Sweden"},{"name":"Laboratory for Molecular Infection Medicine Sweden (MIMS), Ume\u00e5 University, Building 6K and 6L, University Hospital Area, 90187 Ume\u00e5, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, Ume\u00e5 University, Building 6K, 6L University Hospital Area, 90187 Ume\u00e5, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tracy","family":"Nissan","sequence":"additional","affiliation":[{"name":"Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, 10691, Sweden"},{"name":"School of Life Science, University of Sussex, Brighton, BN19RH, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Graf","sequence":"additional","affiliation":[{"name":"Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ji\u0159\u00ed","family":"Nov\u00e1\u010dek","sequence":"additional","affiliation":[{"name":"Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 62500 Brno, Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gemma C","family":"Atkinson","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, Ume\u00e5 University, Building 6K, 6L University Hospital Area, 90187 Ume\u00e5, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcus J O","family":"Johansson","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, Ume\u00e5 University, Building 6K, 6L University Hospital Area, 90187 Ume\u00e5, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel N","family":"Wilson","sequence":"additional","affiliation":[{"name":"Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vasili","family":"Hauryliuk","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, Ume\u00e5 University, Building 6K, 6L University Hospital Area, 90187 Ume\u00e5, Sweden"},{"name":"Laboratory for Molecular Infection Medicine Sweden (MIMS), Ume\u00e5 University, Building 6K and 6L, University Hospital Area, 90187 Ume\u00e5, Sweden"},{"name":"University of Tartu, Institute of Technology, 50411 Tartu, Estonia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,7,12]]},"reference":[{"key":"2020071622551083400_B1","doi-asserted-by":"crossref","first-page":"2165","DOI":"10.1016\/j.jmb.2016.03.022","article-title":"Protein elongation, co-translational folding and targeting","volume":"428","author":"Rodnina","year":"2016","journal-title":"J. Mol. Biol."},{"key":"2020071622551083400_B2","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1007\/s00018-008-8416-4","article-title":"A structural view of translation initiation in bacteria","volume":"66","author":"Simonetti","year":"2009","journal-title":"Cell Mol. Life Sci."},{"key":"2020071622551083400_B3","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1146\/annurev-biochem-060713-035802","article-title":"The scanning mechanism of eukaryotic translation initiation","volume":"83","author":"Hinnebusch","year":"2014","journal-title":"Annu. Rev. Biochem."},{"key":"2020071622551083400_B4","doi-asserted-by":"crossref","first-page":"a013706","DOI":"10.1101\/cshperspect.a013706","article-title":"The elongation, termination, and recycling phases of translation in eukaryotes","volume":"4","author":"Dever","year":"2012","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"2020071622551083400_B5","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1186\/s12864-015-1289-7","article-title":"The evolutionary and functional diversity of classical and lesser-known cytoplasmic and organellar translational GTPases across the tree of life","volume":"16","author":"Atkinson","year":"2015","journal-title":"BMC Genomics"},{"key":"2020071622551083400_B6","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1002\/bip.22832","article-title":"Review: translational GTPases","volume":"105","author":"Maracci","year":"2016","journal-title":"Biopolymers"},{"key":"2020071622551083400_B7","doi-asserted-by":"crossref","first-page":"24061","DOI":"10.1074\/jbc.M109.031625","article-title":"ABC50 promotes translation initiation in mammalian cells","volume":"284","author":"Paytubi","year":"2009","journal-title":"J. Biol. Chem."},{"key":"2020071622551083400_B8","doi-asserted-by":"crossref","first-page":"1259","DOI":"10.1016\/j.str.2018.05.019","article-title":"Crystal structure of ATP-bound human ABCF1 demonstrates a unique conformation of ABC proteins","volume":"26","author":"Qu","year":"2018","journal-title":"Structure"},{"key":"2020071622551083400_B9","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1038\/nature05126","article-title":"Structure of eEF3 and the mechanism of transfer RNA release from the E-site","volume":"443","author":"Andersen","year":"2006","journal-title":"Nature"},{"key":"2020071622551083400_B10","doi-asserted-by":"crossref","first-page":"15838","DOI":"10.1016\/S0021-9258(18)55474-0","article-title":"Protein synthesis in yeast. Structural and functional analysis of the gene encoding elongation factor 3","volume":"265","author":"Sandbaken","year":"1990","journal-title":"J. Biol. Chem."},{"key":"2020071622551083400_B11","doi-asserted-by":"crossref","first-page":"3184","DOI":"10.1002\/j.1460-2075.1995.tb07321.x","article-title":"GCN20, a novel ATP binding cassette protein, and GCN1 reside in a complex that mediates activation of the eIF-2 alpha kinase GCN2 in amino acid-starved cells","volume":"14","author":"Vazquez\u00a0de\u00a0Aldana","year":"1995","journal-title":"EMBO J."},{"key":"2020071622551083400_B12","doi-asserted-by":"crossref","first-page":"132S","DOI":"10.1042\/bst023132s","article-title":"Translational elongation factor 3 (EF-3): a study of its structural and functional divergence in fungi","volume":"23","author":"Ross-Smith","year":"1995","journal-title":"Biochem. Soc. Trans."},{"key":"2020071622551083400_B13","doi-asserted-by":"crossref","first-page":"e0190524","DOI":"10.1371\/journal.pone.0190524","article-title":"Demonstration of translation elongation factor 3 activity from a non-fungal species, Phytophthora infestans","volume":"13","author":"Mateyak","year":"2018","journal-title":"PLoS One"},{"key":"2020071622551083400_B14","article-title":"ABCF ATPases involved in protein synthesis, ribosome assembly and antibiotic Resistance: Structural and functional diversification across the tree of life","author":"Murina","year":"2018","journal-title":"J. Mol. Biol."},{"key":"2020071622551083400_B15","doi-asserted-by":"crossref","first-page":"3055","DOI":"10.1021\/bi00308a032","article-title":"Monoclonal antibody specific for yeast elongation factor 3","volume":"23","author":"Hutchison","year":"1984","journal-title":"Biochemistry"},{"key":"2020071622551083400_B16","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1093\/oxfordjournals.jbchem.a122405","article-title":"Role of yeast peptide elongation factor 3 (EF-3) at the AA-tRNA binding step","volume":"104","author":"Uritani","year":"1988","journal-title":"J. Biochem."},{"key":"2020071622551083400_B17","doi-asserted-by":"crossref","first-page":"10854","DOI":"10.1073\/pnas.1006247107","article-title":"Ribosome recycling step in yeast cytoplasmic protein synthesis is catalyzed by eEF3 and ATP","volume":"107","author":"Kurata","year":"2010","journal-title":"PNAS"},{"key":"2020071622551083400_B18","doi-asserted-by":"crossref","first-page":"3037","DOI":"10.1038\/s41598-019-39403-y","article-title":"Ribosome profiling analysis of eEF3-depleted Saccharomyces cerevisiae","volume":"9","author":"Kasari","year":"2019","journal-title":"Sci. Rep."},{"key":"2020071622551083400_B19","doi-asserted-by":"crossref","first-page":"20473","DOI":"10.1074\/jbc.270.35.20473","article-title":"The elongation factor 3 unique in higher fungi and essential for protein biosynthesis is an E site factor","volume":"270","author":"Triana-Alonso","year":"1995","journal-title":"J. Biol. Chem."},{"key":"2020071622551083400_B20","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1038\/ng0297-137","article-title":"Complete inventory of the yeast ABC proteins","volume":"15","author":"Decottignies","year":"1997","journal-title":"Nat. Genet."},{"key":"2020071622551083400_B21","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1002\/(SICI)1097-0061(19980915)14:12<1105::AID-YEA313>3.0.CO;2-Y","article-title":"A highly conserved intraspecies homolog of the Saccharomyces cerevisiae elongation factor-3 encoded by the HEF3 gene","volume":"14","author":"Maurice","year":"1998","journal-title":"Yeast"},{"key":"2020071622551083400_B22","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1038\/nature02424","article-title":"Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae","volume":"428","author":"Kellis","year":"2004","journal-title":"Nature"},{"key":"2020071622551083400_B23","doi-asserted-by":"crossref","first-page":"e1000213","DOI":"10.1371\/journal.pbio.1000213","article-title":"Rational extension of the ribosome biogenesis pathway using network-guided genetics","volume":"7","author":"Li","year":"2009","journal-title":"PLoS Biol."},{"key":"2020071622551083400_B24","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1016\/S0092-8674(00)81565-2","article-title":"Molecular basis of a yeast prion species barrier","volume":"100","author":"Santoso","year":"2000","journal-title":"Cell"},{"key":"2020071622551083400_B25","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/S0092-8674(01)00440-8","article-title":"Multiple Gln\/Asn-rich prion domains confer susceptibility to induction of the yeast [PSI(+)] prion","volume":"106","author":"Osherovich","year":"2001","journal-title":"Cell"},{"key":"2020071622551083400_B26","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1016\/j.jmb.2007.01.070","article-title":"Evolution of budding yeast prion-determinant sequences across diverse fungi","volume":"368","author":"Harrison","year":"2007","journal-title":"J. Mol. Biol."},{"key":"2020071622551083400_B27","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1111\/j.1365-2958.2011.07555.x","article-title":"Antibiotic-induced ribosomal assembly defects result from changes in the synthesis of ribosomal proteins","volume":"80","author":"Siibak","year":"2011","journal-title":"Mol. Microbiol."},{"key":"2020071622551083400_B28","volume-title":"Methods in Yeast Genetics: a Cold Spring Harbor Laboratory Course Manual","author":"Amberg","year":"2005"},{"key":"2020071622551083400_B29","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1007\/978-1-4939-6518-2_13","article-title":"Determining if an mRNA is a substrate of nonsense-mediated mRNA decay in Saccharomyces cerevisiae","volume":"1507","author":"Johansson","year":"2017","journal-title":"Methods Mol. Biol."},{"key":"2020071622551083400_B30","doi-asserted-by":"crossref","first-page":"953","DOI":"10.1002\/(SICI)1097-0061(199807)14:10<953::AID-YEA293>3.0.CO;2-U","article-title":"Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae","volume":"14","author":"Longtine","year":"1998","journal-title":"Yeast"},{"key":"2020071622551083400_B31","doi-asserted-by":"crossref","first-page":"e130","DOI":"10.1093\/nar\/gku616","article-title":"Inducible, tightly regulated and growth condition-independent transcription factor in Saccharomyces cerevisiae","volume":"42","author":"Ottoz","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2020071622551083400_B32","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1251\/bpo71","article-title":"Ribosome formation from subunits studied by stopped-flow and Rayleigh light scattering","volume":"6","author":"Antoun","year":"2004","journal-title":"Biol. Proced. Online"},{"key":"2020071622551083400_B33","doi-asserted-by":"crossref","first-page":"14082","DOI":"10.1074\/jbc.M211818200","article-title":"The quaternary structure of DNA polymerase epsilon from Saccharomyces cerevisiae","volume":"278","author":"Chilkova","year":"2003","journal-title":"J. Biol. Chem."},{"key":"2020071622551083400_B34","doi-asserted-by":"crossref","first-page":"e06980","DOI":"10.7554\/eLife.06980","article-title":"Measuring the optimal exposure for single particle cryo-EM using a 2.6 A reconstruction of rotavirus VP6","volume":"4","author":"Grant","year":"2015","journal-title":"Elife"},{"key":"2020071622551083400_B35","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jsb.2015.11.003","article-title":"Gctf: Real-time CTF determination and correction","volume":"193","author":"Zhang","year":"2016","journal-title":"J. Struct. Biol."},{"key":"2020071622551083400_B36","doi-asserted-by":"crossref","first-page":"e18722","DOI":"10.7554\/eLife.18722","article-title":"Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2","volume":"5","author":"Kimanius","year":"2016","journal-title":"Elife"},{"key":"2020071622551083400_B37","doi-asserted-by":"crossref","first-page":"e42166","DOI":"10.7554\/eLife.42166","article-title":"New tools for automated high-resolution cryo-EM structure determination in RELION-3","volume":"7","author":"Zivanov","year":"2018","journal-title":"Elife"},{"key":"2020071622551083400_B38","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1107\/S0907444909052925","article-title":"PHENIX: a comprehensive Python-based system for macromolecular structure solution","volume":"66","author":"Adams","year":"2010","journal-title":"Acta Crystallogr. Sect. D Biol. Crystallogr."},{"key":"2020071622551083400_B39","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1038\/nmeth.2115","article-title":"Prevention of overfitting in cryo-EM structure determination","volume":"9","author":"Scheres","year":"2012","journal-title":"Nat. Methods"},{"key":"2020071622551083400_B40","doi-asserted-by":"crossref","first-page":"D313","DOI":"10.1093\/nar\/gkw1132","article-title":"The SWISS-MODEL repository-new features and functionality","volume":"45","author":"Bienert","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2020071622551083400_B41","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera\u2013a visualization system for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J. Comput. Chem."},{"key":"2020071622551083400_B42","doi-asserted-by":"crossref","first-page":"2126","DOI":"10.1107\/S0907444904019158","article-title":"Coot: model-building tools for molecular graphics","volume":"60","author":"Emsley","year":"2004","journal-title":"Acta Crystallogr. Sect. D Biol. Crystallogr."},{"key":"2020071622551083400_B43","doi-asserted-by":"crossref","first-page":"8978","DOI":"10.1073\/pnas.1808535115","article-title":"Structural basis for antibiotic resistance mediated by the Bacillus subtilis ABCF ATPase VmlR","volume":"115","author":"Crowe-McAuliffe","year":"2018","journal-title":"PNAS"},{"key":"2020071622551083400_B44","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1107\/S1399004714021683","article-title":"Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions","volume":"71","author":"Brown","year":"2015","journal-title":"Acta Crystallogr. Sect. D Biol. Crystallogr."},{"key":"2020071622551083400_B45","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1107\/S0907444909042073","article-title":"MolProbity: all-atom structure validation for macromolecular crystallography","volume":"66","author":"Chen","year":"2010","journal-title":"Acta Crystallogr. Sect. D Biol. Crystallogr."},{"key":"2020071622551083400_B46","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1002\/pro.3235","article-title":"UCSF ChimeraX: Meeting modern challenges in visualization and analysis","volume":"27","author":"Goddard","year":"2018","journal-title":"Protein Sci."},{"key":"2020071622551083400_B47","article-title":"FastQC: a quality control tool for high throughput sequence data","author":"Andrews","year":"2010"},{"key":"2020071622551083400_B48","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet. J."},{"key":"2020071622551083400_B49","doi-asserted-by":"crossref","first-page":"1650","DOI":"10.1038\/nprot.2016.095","article-title":"Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown","volume":"11","author":"Pertea","year":"2016","journal-title":"Nat. Protoc."},{"key":"2020071622551083400_B50","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq\u2013a Python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"2020071622551083400_B51","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"2020071622551083400_B52","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"2020071622551083400_B53","doi-asserted-by":"crossref","first-page":"D183","DOI":"10.1093\/nar\/gkw1138","article-title":"PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements","volume":"45","author":"Mi","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2020071622551083400_B54","doi-asserted-by":"crossref","first-page":"5767","DOI":"10.1093\/nar\/22.25.5767","article-title":"Regulatable promoters of Saccharomyces cerevisiae: comparison of transcriptional activity and their use for heterologous expression","volume":"22","author":"Mumberg","year":"1994","journal-title":"Nucleic Acids Res."},{"key":"2020071622551083400_B55","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1038\/nsmb.2740","article-title":"The ABC-F protein EttA gates ribosome entry into the translation elongation cycle","volume":"21","author":"B\u00f6el","year":"2014","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2020071622551083400_B56","doi-asserted-by":"crossref","first-page":"1030","DOI":"10.1038\/13732","article-title":"A generic protein purification method for protein complex characterization and proteome exploration","volume":"17","author":"Rigaut","year":"1999","journal-title":"Nat. Biotechnol."},{"key":"2020071622551083400_B57","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1038\/nsmb.3396","article-title":"Structure of the 40S-ABCE1 post-splitting complex in ribosome recycling and translation initiation","volume":"24","author":"Heuer","year":"2017","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2020071622551083400_B58","doi-asserted-by":"crossref","first-page":"7962","DOI":"10.1074\/jbc.M707347200","article-title":"X-ray structure of the complete ABC enzyme ABCE1 from Pyrococcus abyssi","volume":"283","author":"Karcher","year":"2008","journal-title":"J. Biol. Chem."},{"key":"2020071622551083400_B59","doi-asserted-by":"crossref","first-page":"a032698","DOI":"10.1101\/cshperspect.a032698","article-title":"Ribosome profiling: global views of translation","volume":"11","author":"Ingolia","year":"2018","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"2020071622551083400_B60","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1016\/j.molcel.2018.12.009","article-title":"High-Resolution ribosome profiling defines discrete ribosome elongation states and translational regulation during cellular stress","volume":"73","author":"Wu","year":"2019","journal-title":"Mol. Cell"},{"key":"2020071622551083400_B61","doi-asserted-by":"crossref","first-page":"e01257","DOI":"10.7554\/eLife.01257","article-title":"Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments","volume":"3","author":"Lareau","year":"2014","journal-title":"Elife"},{"key":"2020071622551083400_B62","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1016\/j.molcel.2017.03.003","article-title":"eIF5A functions globally in translation elongation and termination","volume":"66","author":"Schuller","year":"2017","journal-title":"Mol. Cell"},{"key":"2020071622551083400_B63","doi-asserted-by":"crossref","first-page":"872","DOI":"10.1016\/j.cell.2015.07.041","article-title":"Rli1\/ABCE1 recycles terminating ribosomes and controls translation reinitiation in 3\u2032UTRs in vivo","volume":"162","author":"Young","year":"2015","journal-title":"Cell"},{"key":"2020071622551083400_B64","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1016\/j.celrep.2014.06.036","article-title":"Genome-wide translational changes induced by the prion [PSI+]","volume":"8","author":"Baudin-Baillieu","year":"2014","journal-title":"Cell Rep."},{"key":"2020071622551083400_B65","doi-asserted-by":"crossref","first-page":"3332","DOI":"10.1093\/nar\/gkv171","article-title":"Stabilization of eukaryotic ribosomal termination complexes by deacylated tRNA","volume":"43","author":"Susorov","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2020071622551083400_B66","doi-asserted-by":"crossref","first-page":"691","DOI":"10.1261\/rna.5147804","article-title":"Leaky termination at premature stop codons antagonizes nonsense-mediated mRNA decay in S. cerevisiae","volume":"10","author":"Keeling","year":"2004","journal-title":"RNA"},{"key":"2020071622551083400_B67","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1038\/nmeth.2646","article-title":"pLogo: a probabilistic approach to visualizing sequence motifs","volume":"10","author":"O'Shea","year":"2013","journal-title":"Nat. Methods"},{"key":"2020071622551083400_B68","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1038\/sj.emboj.7600541","article-title":"Biogenesis of cytosolic ribosomes requires the essential iron-sulphur protein Rli1p and mitochondria","volume":"24","author":"Kispal","year":"2005","journal-title":"EMBO J."},{"key":"2020071622551083400_B69","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1016\/j.molcel.2009.12.034","article-title":"The role of ABCE1 in eukaryotic posttermination ribosomal recycling","volume":"37","author":"Pisarev","year":"2010","journal-title":"Mol. Cell"},{"key":"2020071622551083400_B70","doi-asserted-by":"crossref","first-page":"744","DOI":"10.1038\/nsmb.2308","article-title":"Proofreading of pre-40S ribosome maturation by a translation initiation factor and 60S subunits","volume":"19","author":"Lebaron","year":"2012","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2020071622551083400_B71","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1038\/35002118","article-title":"The joining of ribosomal subunits in eukaryotes requires eIF5B","volume":"403","author":"Pestova","year":"2000","journal-title":"Nature"},{"key":"2020071622551083400_B72","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1038\/embor.2009.70","article-title":"Eukaryotic initiation factor 6 mediates a continuum between 60S ribosome biogenesis and translation","volume":"10","author":"Miluzio","year":"2009","journal-title":"EMBO Rep."},{"key":"2020071622551083400_B73","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1111\/j.1365-2443.2011.01510.x","article-title":"Yeast prion protein New1 can break Sup35 amyloid fibrils into fragments in an ATP-dependent manner","volume":"16","author":"Inoue","year":"2011","journal-title":"Genes Cells"},{"key":"2020071622551083400_B74","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1007\/BF00330984","article-title":"A positive selection for mutants lacking orotidine-5\u2032-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance","volume":"197","author":"Boeke","year":"1984","journal-title":"Mol. Gen. Genet."},{"key":"2020071622551083400_B75","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1002\/(SICI)1097-0061(19980130)14:2<115::AID-YEA204>3.0.CO;2-2","article-title":"Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications","volume":"14","author":"Brachmann","year":"1998","journal-title":"Yeast"},{"key":"2020071622551083400_B76","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1038\/nature02046","article-title":"Global analysis of protein expression in yeast","volume":"425","author":"Ghaemmaghami","year":"2003","journal-title":"Nature"},{"key":"2020071622551083400_B77","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1006\/meth.2001.1183","article-title":"The tandem affinity purification (TAP) method: a general procedure of protein complex purification","volume":"24","author":"Puig","year":"2001","journal-title":"Methods"},{"key":"2020071622551083400_B78","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1093\/genetics\/122.1.19","article-title":"A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae","volume":"122","author":"Sikorski","year":"1989","journal-title":"Genetics"},{"key":"2020071622551083400_B79","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/0378-1119(92)90454-W","article-title":"Multifunctional yeast high-copy-number shuttle vectors","volume":"110","author":"Christianson","year":"1992","journal-title":"Gene"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/47\/16\/8807\/31234476\/gkz600.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/47\/16\/8807\/31234476\/gkz600.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,23]],"date-time":"2022-09-23T18:14:38Z","timestamp":1663956878000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/47\/16\/8807\/5531767"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,7,12]]},"references-count":79,"journal-issue":{"issue":"16","published-online":{"date-parts":[[2019,7,12]]},"published-print":{"date-parts":[[2019,9,19]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkz600","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,9,19]]},"published":{"date-parts":[[2019,7,12]]}}}