References

Abeyrathne, P.D., Koh, C.S., Grant, T., Grigorieff, N., & Korostelev, A.A. (2016). Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome. eLife, 5, e14874.

Adams, P.D., Afonine, P.V., Bunkóczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.-W., Kapral, G.J., Grosse-Kunstleve, R.W., et al. (2010). PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. Sect. D Biol. Crystallogr., 66, 213-221.

Afonina, Z.A., Myasnikov, A.G., Khabibullina, N.F., Belorusova, A.Y., Menetret, J.-F., Vasiliev, V.D., Klaholz, B.P., Shirokov, V.A., & Spirin, A.S. (2013). Topology of mRNA chain in isolated eukaryotic double-row polyribosomes. Biochem., 78, 445-454.

Afonina, Z.A., Myasnikov, A.G., Shirokov, V.A., Klaholz, B.P., & Spirin, A.S. (2014). Formation of circular polyribosomes on eukaryotic mRNA without cap-structure and poly(A)-tail: a cryo electron tomography study. Nucleic Acids Res., 42, 9461-9469.

Agirrezabala, X., Lei, J., Brunelle, J.L., Ortiz-Meoz, R.F., Green, R., & Frank, J. (2008). Visualization of the Hybrid State of tRNA Binding Promoted by Spontaneous Ratcheting of the Ribosome. Mol. Cell, 32, 190-197.

Alejo, J.L., & Blanchard, S.C. (2017). Miscoding-induced stalling of substrate translocation on the bacterial ribosome. Proc. Natl. Acad. Sci., 114, 201707539.

Allen, G.S., Zavialov, A., Gursky, R., Ehrenberg, M., & Frank, J. (2005). The Cryo-EM Structure of a Translation Initiation Complex from Escherichia coli. Cell, 121, 703-712.

Amunts, A., Brown, A., Toots, J., Scheres, S.H.W., & Ramakrishnan, V. (2015). The structure of the human mitochondrial ribosome. Science, 348, 95-98.

Andersen, C.B.F., Becker, T., Blau, M., Anand, M., Halic, M., Balar, B., Mielke, T., Boesen, T., Pedersen, J.S., Spahn, C.M.T., et al. (2006). Structure of eEF3 and the mechanism of transfer RNA release from the E-site. Nature, 443, 663-668.

Antoun, A., Pavlov, M.Y., Andersson, K., Tenson, T., & Ehrenberg, M. (2003). The roles of initiation factor 2 and guanosine triphosphate in initiation of protein synthesis. EMBO J., 22, 5593-5601.

Archer, S.K., Shirokikh, N.E., Beilharz, T.H., & Preiss, T. (2016). Dynamics of ribosome scanning and recycling revealed by translation complex profiling. Nature, 535, 570-574.

Bah, A., Vernon, R.M., Siddiqui, Z., Krzeminski, M., Muhandiram, R., Zhao, C., Sonenberg, N., Kay, L.E., & Forman-Kay, J.D. (2015). Folding of an intrinsically disordered protein by phosphorylation as a regulatory switch. Nature, 519, 106-109.

Ban, N., Beckmann, R., Cate, J.H.D., Dinman, J.D., Dragon, F., Ellis, S.R., Lafontaine, D.L.J., Lindahl, L., Liljas, A., Lipton, J.M., et al. (2014). A new system for naming ribosomal proteins. Curr. Opin. Struct. Biol., 24, 165-169.

Bandi, H.R., Ferrari, S., Krieg, J., Meyer, H.E., & Thomas, G. (1993). Identification of 40 S ribosomal protein S6 phosphorylation sites in Swiss mouse 3T3 fibroblasts stimulated with serum. J. Biol. Chem., 268, 4530-4533.

Bartesaghi, A., Aguerrebere, C., Falconieri, V., Banerjee, S., Earl, L.A., Zhu, X., Grigorieff, N., Milne, J.L.S., Sapiro, G., Wu, X., et al. (2018). Atomic Resolution Cryo-EM Structure of β-Galactosidase. Structure, 26, 848-856.e3.

Barth-Baus, D., Stratton, C.A., Parrott, L., Myerson, H., Meyuhas, O., Templeton, D.J., Landreth, G.E., & Hensold, J.O. (2002). S6 phosphorylation-independent pathways regulate translation of 5’-terminal oligopyrimidine tract-containing mRNAs in differentiating hematopoietic cells. Nucleic Acids Res., 30, 1919-1928.

Becker, T., Armache, J.-P., Jarasch, A., Anger, A.M., Villa, E., Sieber, H., Motaal, B.A., Mielke, T., Berninghausen, O., & Beckmann, R. (2011). Structure of the no-go mRNA decay complex Dom34–Hbs1 bound to a stalled 80S ribosome. Nat. Struct. Mol. Biol., 18, 715-720.

Behrmann, E., Loerke, J., Budkevich, T.V., Yamamoto, K., Schmidt, A., Penczek, P.A., Vos, M.R., Bürger, J., Mielke, T., Scheerer, P., et al. (2015). Structural Snapshots of Actively Translating Human Ribosomes. Cell, 161, 845-857.

Belandia, B., Brautigan, D., & Martín-Pérez, J. (1994). Attenuation of ribosomal protein S6 phosphatase activity in chicken embryo fibroblasts transformed by Rous sarcoma virus. Mol. Cell. Biol., 14, 200-206.

Belardinelli, R., Sharma, H., Peske, F., Wintermeyer, W., & Rodnina, M.V. (2016). Translocation as continuous movement through the ribosome. RNA Biol., 13, 1-7.

Ben-Shem, A., Jenner, L., Yusupova, G., & Yusupov, M. (2010). Crystal Structure of the Eukaryotic Ribosome. Science, 330, 1203-1209.

Ben-Shem, A., Garreau de Loubresse, N., Melnikov, S., Jenner, L., Yusupova, G., & Yusupov, M. (2011). The structure of the eukaryotic ribosome at 3.0 Å resolution. Science, 334, 1524-1529.

Berman, H.M. (2000). The Protein Data Bank. Nucleic Acids Res., 28, 235-242.

Bhat, M., Robichaud, N., Hulea, L., Sonenberg, N., Pelletier, J., & Topisirovic, I. (2015). Targeting the translation machinery in cancer. Nat. Rev. Drug Discov., 14, 261-278.

Blanchard, S.C., Kim, H.D., Gonzalez, R.L., Puglisi, J.D., & Chu, S. (2004). tRNA dynamics on the ribosome during translation. Proc. Natl. Acad. Sci., 101, 12893-12898.

Bommer, U., Burkhardt, N., Junemann, R., Spahn, C.M.T., Triana-Alonso, & F. Nierhaus, K.H. (1997). Ribosomes and polysomes. In Subcellular Fractionation: A Practical Approach, J. Graham and D. Rickwood, Eds., (Washington, DC: IRL Press), pp. 271-301.

Bourne, H.R., Sanders, D.A., & McCormick, F. (1991). The GTPase superfamily: conserved structure and molecular mechanism. Nature, 349, 117-127.

Brandt, F., Carlson, L.-A.A., Hartl, F.U., Baumeister, W., & Grünewald, K. (2010). The Three-Dimensional Organization of Polyribosomes in Intact Human Cells. Mol. Cell, 39, 560-569.

Brilot, A.F., Korostelev, A.A., Ermolenko, D.N., & Grigorieff, N. (2013). Structure of the ribosome with elongation factor G trapped in the pretranslocation state. Proc. Natl. Acad. Sci., 110, 20994-20999.

Budkevich, T., Giesebrecht, J., Altman, R.B., Munro, J.B., Mielke, T., Nierhaus, K.H., Blanchard, S.C., & Spahn, C.M.T. (2011). Structure and Dynamics of the Mammalian Ribosomal Pretranslocation Complex. Mol. Cell, 44, 214-224.

Budkevich, T.V., El’skaya, A.V., & Nierhaus, K.H. (2008). Features of 80S mammalian ribosome and its subunits. Nucleic Acids Res., 36, 4736-4744.

Budkevich, T.V., Giesebrecht, J., Behrmann, E., Loerke, J., Ramrath, D.J.F., Mielke, T., Ismer, J., Hildebrand, P.W., Tung, C.S., Nierhaus, K.H., et al. (2014). Regulation of the mammalian elongation cycle by subunit rolling: A eukaryotic-specific ribosome rearrangement. Cell, 158, 121-131.

Carter, A.P., Clemons, W.M., Brodersen, D.E., Morgan-Warren, R.J., Hartsch, T., Wimberly, B.T., & Ramakrishnan, V. (2001). Crystal structure of an initiation factor bound to the 30S ribosomal subunit. Science, 291, 498-501.

Chaisuparat, R., Rojanawatsirivej, S., & Yodsanga, S. (2013). Ribosomal Protein S6 Phosphorylation is Associated with Epithelial Dysplasia and Squamous Cell Carcinoma of the Oral Cavity. Pathol. Oncol. Res., 19, 189-193.

Chauvin, C., Koka, V., Nouschi, A., Mieulet, V., Hoareau-Aveilla, C., Dreazen, A., Cagnard, N., Carpentier, W., Kiss, T., Meyuhas, O., et al. (2014). Ribosomal protein S6 kinase activity controls the ribosome biogenesis transcriptional program. Oncogene, 33, 474-483.

Chen, J.Z., & Grigorieff, N. (2007). SIGNATURE: A single-particle selection system for molecular electron microscopy. J. Struct. Biol., 157, 168-173.

Chen, C., Cui, X., Beausang, J.F., Zhang, H., Farrell, I., Cooperman, B.S., & Goldman, Y.E. (2016). Elongation factor G initiates translocation through a power stroke. Proc. Natl. Acad. Sci., 113, 7515-7520.

Chen, J., Petrov, A., Tsai, A., O’Leary, S.E., & Puglisi, J.D. (2013). Coordinated conformational and compositional dynamics drive ribosome translocation. Nat. Struct. Mol. Biol., 20, 718-727.

Chen, V.B., Arendall, W.B., Headd, J.J., Keedy, D.A., Immormino, R.M., Kapral, G.J., Murray, L.W., Richardson, J.S., & Richardson, D.C. (2010). MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. Sect. D Biol. Crystallogr., 66, 12-21.

Cheng, Y., Grigorieff, N., Penczek, P.A., & Walz, T. (2015). A Primer to Single-Particle Cryo-Electron Microscopy. Cell, 161, 438-449.

Chou, F.-C., Sripakdeevong, P., Dibrov, S.M., Hermann, T., & Das, R. (2012). Correcting pervasive errors in RNA crystallography through enumerative structure prediction. Nat. Methods, 10, 74-76.

Connell, S.R., Takemoto, C., Wilson, D.N., Wang, H., Murayama, K., Terada, T., Shirouzu, M., Rost, M., Schüler, M., Giesebrecht, J., et al. (2007). Structural Basis for Interaction of the Ribosome with the Switch Regions of GTP-Bound Elongation Factors. Mol. Cell, 25, 751-764.

Cornish, P.V., Ermolenko, D.N., Noller, H.F., & Ha, T. (2008). Spontaneous Intersubunit Rotation in Single Ribosomes. Mol. Cell, 30, 578-588.

Crick, F. (1970). Central Dogma of Molecular Biology. Nature, 227, 561-563.

Cukras, A.R., Southworth, D.R., Brunelle, J.L., Culver, G.M., & Green, R. (2003). Ribosomal proteins S12 and S13 function as control elements for translocation of the mRNA:tRNA complex. Mol. Cell, 12, 321-328.

Czworkowski, J., & Moore, P.B. (1997). The conformational properties of elongation factor G and the mechanism of translocation. Biochemistry, 36, 10327-10334.

Czworkowski, J., Wang, J., Steitz, T.A., & Moore, P.B. (1994). The crystal structure of elongation factor G complexed with GDP, at 2.7 A resolution. EMBO J., 13, 3661-3668.

Danev, R., & Baumeister, W. (2017). Expanding the boundaries of cryo-EM with phase plates. Curr. Opin. Struct. Biol., 46, 87-94.

Dauden, M.I., Kosinski, J., Kolaj‐Robin, O., Desfosses, A., Ori, A., Faux, C., Hoffmann, N.A., Onuma, O.F., Breunig, K.D., Beck, M., et al. (2017). Architecture of the yeast Elongator complex. EMBO Rep., 18, 264-279.

Davydova, E.K., & Ovchinnikov, L.P. (1990). ADP-ribosylated elongation factor 2 (ADP-ribosyl-EF-2) is unable to promote translocation within the ribosome. FEBS Lett., 261, 350-352.

Davydova, E.K., Malinin, N.L., & Ovchinnikov, L.P. (1993). Ribosomes terminated in vitro are in a tight association with non-phosphorylated elongation factor 2 (eEF-2) and GDP. Eur. J. Biochem., 215, 291-296.

Dubochet, J., Adrian, M., Chang, J.J., Homo, J.C., Lepault, J., McDowall, A.W., & Schultz, P. (1988). Cryo-electron microscopy of vitrified specimens. Q. Rev. Biophys., 21, 129-228.

Duncan, R., & McConkey, E.H. (1982). Preferential Utilization of Phosphorylated 40‐S Ribosomal Subunits during Initiation Complex Formation. Eur. J. Biochem., 123, 535-538.

Dunkle, J.A., Wang, L., Feldman, M.B., Pulk, A., Chen, V.B., Kapral, G.J., Noeske, J., Richardson, J.S., Blanchard, S.C., & Cate, J.H.D. (2011). Structures of the Bacterial Ribosome in Classical and Hybrid States of tRNA Binding. Science, 332, 981-984.

Egerton, R.F., Li, P., & Malac, M. (2004). Radiation damage in the TEM and SEM. Micron, 35, 399-409.

Eliseev, B., Yeramala, L., Leitner, A., Karuppasamy, M., Raimondeau, E., Huard, K., Alkalaeva, E., Aebersold, R., & Schaffitzel, C. (2018). Structure of a human cap-dependent 48S translation pre-initiation complex. Nucleic Acids Res., 46, 2678-2689.

Emsley, P., & Cowtan, K. (2004). Coot: Model-building tools for molecular graphics. Acta Crystallogr. Sect. D Biol. Crystallogr., 60, 2126-2132.

Fasken, M.B., & Corbett, A.H. (2009). Mechanisms of nuclear mRNA quality control. RNA Biol., 6, 237-241.

Ferguson, A., Wang, L., Altman, R.B., Terry, D.S., Juette, M.F., Burnett, B.J., Alejo, J.L., Dass, R.A., Parks, M.M., Vincent, C.T., et al. (2015). Functional Dynamics within the Human Ribosome Regulate the Rate of Active Protein Synthesis. Mol. Cell, 60, 475-486.

Flis, J., Holm, M., Rundlet, E.J., Loerke, J., Hilal, T., Dabrowski, M., Bürger, J., Mielke, T., Blanchard, S.C., Spahn, C.M.T., et al. (2018). tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis. Cell Rep., 25, 2676-2688.e7.

Frank, J., & Agrawal, R.K. (2000). A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature, 406, 318-322.

Frank, J., Penczek, P., & Liu, W. (1992). Alignment, classification, and three-dimensional reconstruction of single particles embedded in ice. Scanning Microsc. Suppl., 6, 11-20; discussion 20-22.

Frank, J., Radermacher, M., Penczek, P., Zhu, J., Li, Y., Ladjadj, M., & Leith, A. (1996). SPIDER and WEB: Processing and Visualization of Images in 3D Electron Microscopy and Related Fields. J. Struct. Biol., 116, 190-199.

Frauenfelder, H., Sligar, S.G., & Wolynes, P.G. (1991). The energy landscapes and motions of proteins. Science, 254, 1598-1603.

Gao, H., Zhou, Z., Rawat, U., Huang, C., Bouakaz, L., Wang, C., Cheng, Z., Liu, Y., Zavialov, A., Gursky, R., et al. (2007). RF3 Induces Ribosomal Conformational Changes Responsible for Dissociation of Class I Release Factors. Cell, 129, 929-941.

Gao, Y.-G., Selmer, M., Dunham, C.M., Weixlbaumer, A., Kelley, A.C., & Ramakrishnan, V. (2009). The Structure of the Ribosome with Elongation Factor G Trapped in the Posttranslocational State. Science, 326, 694-699.

Gavrilova, L.P., & Spirin, A.S. (1971). Stimulation of non-enzymic translocation in ribosomes by p-chloromercuribenzoate. FEBS Lett., 17, 324-326.

Gavrilova, L.P., Kostiashkina, O.E., Koteliansky, V.E., Rutkevitch, N.M., & Spirin, A.S. (1976). Factor-free and factor-dependent systems of translation of polyuridylic acid by Escherichia coli ribosomes. J. Mol. Biol., 101, 537-552.

Gesteland, R.F., Cech, T.R., & Atkins, J.F. (1999). The RNA World (Cold Spring Harbor, New York). Cold Spring Harbor Laboratory Press.

Granot, Z., Swisa, A., Magenheim, J., Stolovich-Rain, M., Fujimoto, W., Manduchi, E., Miki, T., Lennerz, J.K., Stoeckert, C.J., Meyuhas, O., et al. (2009). LKB1 regulates pancreatic beta cell size, polarity, and function. Cell Metab., 10, 296-308.

Greber, B.J., Bieri, P., Leibundgut, M., Leitner, A., Aebersold, R., Boehringer, D., & Ban, N. (2015). The complete structure of the 55S mammalian mitochondrial ribosome. Science, 348, 303-308.

Gressner, A.M., & Wool, I.G. (1974). The stimulation of the phosphorylation of ribosomal protein S6 by cycloheximide and puromycin. Biochem. Biophys. Res. Commun., 60, 1482-1490.

Hallinan, T., Eden, E., & North, R. (1962). The Structure and Composition of Rat Reticulocytes. Blood, 20, 50-63.

Hansen, J.L., Schmeing, T.M., Moore, P.B., & Steitz, T.A. (2002). Structural insights into peptide bond formation. Proc. Natl. Acad. Sci. U. S. A., 99, 11670-11675.

Harauz, G., & van Heel, M. (1986). Exact Filters for General Geometry Three Dimensional Reconstruction. Optik (Stuttg)., 74, 146-156.

Hartman, H., & Smith, T.F. (2010). GTPases and the origin of the ribosome. Biol. Direct, 5, 36.

Hashem, Y., & Frank, J. (2018). The Jigsaw Puzzle of mRNA Translation Initiation in Eukaryotes: A Decade of Structures Unraveling the Mechanics of the Process. Annu. Rev. Biophys., 47, 125-151.

Hashem, Y., Des Georges, A., Dhote, V., Langlois, R., Liao, H.Y., Grassucci, R.A., Hellen, C.U.T., Pestova, T.V., & Frank, J. (2013). Structure of the mammalian ribosomal 43S preinitiation complex bound to the scanning factor DHX29. Cell, 153, 1108-1119.

van Heel, M., & Schatz, M. (2005). Fourier shell correlation threshold criteria. J. Struct. Biol., 151, 250-262.

Hilal, T., Yamamoto, H., Loerke, J., Bürger, J., Mielke, T., & Spahn, C.M.T. (2016). Structural insights into ribosomal rescue by Dom34 and Hbs1 at near-atomic resolution. Nat. Commun., 7, 13521.

Hirashima, A., & Kaji, A. (1970). Factor dependent breakdown of polysomes. Biochem. Biophys. Res. Commun., 41, 877-883.

Horan, L.H., & Noller, H.F. (2007). Intersubunit movement is required for ribosomal translocation. Proc. Natl. Acad. Sci. U. S. A., 104, 4881-4885.

Hutchinson, J.A., Shanware, N.P., Chang, H., & Tibbetts, R.S. (2011). Regulation of ribosomal protein S6 phosphorylation by casein kinase 1 and protein phosphatase 1. J. Biol. Chem., 286, 8688-8696.

Inoue-Yokosawa, N., & Kaziro, Y. (1974). The role of guanosine triphosphate in translocation reaction catalyzed by elongation factor G. Biochem. Biophys. Res. Commun., 60, 4321-4323.

Isken, O., & Maquat, L.E. (2007). Quality control of eukaryotic mRNA: Safeguarding cells from abnormal mRNA function. Genes Dev., 21, 1833-1856.

Jackson, R.J., Hellen, C.U.T., & Pestova, T.V. (2010). The mechanism of eukaryotic translation initiation and principles of its regulation. Nat. Rev. Mol. Cell Biol., 11, 113-127.

Jackson, R.J., Hellen, C.U.T., & Pestova, T.V. (2012). Termination and post-termination events in eukaryotic translation. Adv. Protein Chem. Struct. Biol., 86, 45-93.

Jagannathan, S., Nwosu, C., & Nicchitta, C.V. (2011). Analyzing mRNA Localization to the Endoplasmic Reticulum via Cell Fractionation. In Methods in Molecular Biology (Humana Press, Totowa, NJ), pp. 301-321.

de Jong, A.F., & Van Dyck, D. (1993). Ultimate resolution and information in electron microscopy II. The information limit of transmission electron microscopes. Ultramicroscopy, 49, 66-80.

Juhling, F., Morl, M., Hartmann, R.K., Sprinzl, M., Stadler, P.F., & Putz, J. (2009). tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res., 37, D159-D162.

Karbstein, K. (2011). Inside the 40S ribosome assembly machinery. Curr. Opin. Chem. Biol., 15, 657-663.

Khatter, H., Myasnikov, A.G., Natchiar, S.K., & Klaholz, B.P. (2015). Structure of the human 80S ribosome. Nature, 520, 640-645.

Kim, S.-H., Jang, Y.H., Chau, G.C., Pyo, S., & Um, S.H. (2013). Prognostic significance and function of phosphorylated ribosomal protein S6 in esophageal squamous cell carcinoma. Int. J. Cancer, 132, 19-30.

Kolupaeva, V.G., Unbehaun, A., Lomakin, I.B., Hellen, C.U.T., & Pestova, T.V. (2005). Binding of eukaryotic initiation factor 3 to ribosomal 40S subunits and its role in ribosomal dissociation and anti-association. RNA, 11, 470-486.

Kozak, M. (1999). Initiation of translation in prokaryotes and eukaryotes. Gene, 234, 187-208.

Kuhlbrandt, W. (2014). The Resolution Revolution. Science, 343, 1443-1444.

Kumar, P., Hellen, C.U.T., & Pestova, T.V. (2016). Toward the mechanism of eIF4F-mediated ribosomal attachment to mammalian capped mRNAs. Genes Dev., 30, 1573-1588.

Lee, A.S.Y., Kranzusch, P.J., Doudna, J.A., & Cate, J.H.D. (2016). eIF3d is an mRNA cap-binding protein that is required for specialized translation initiation. Nature, 536, 96-99.

Li, X., Mooney, P., Zheng, S., Booth, C.R., Braunfeld, M.B., Gubbens, S., Agard, D.A., & Cheng, Y. (2013). Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat. Methods, 10, 584-590.

Li, Y., Mitsuhashi, S., Ikejo, M., Miura, N., Kawamura, T., Hamakubo, T., & Ubukata, M. (2012). Relationship between ATM and Ribosomal Protein S6 Revealed by the Chemical Inhibition of Ser/Thr Protein Phosphatase Type 1. Biosci. Biotechnol. Biochem., 76, 486-494.

Liao, H.Y., Hashem, Y., & Frank, J. (2015). Efficient Estimation of Three-Dimensional Covariance and its Application in the Analysis of Heterogeneous Samples in Cryo-Electron Microscopy. Structure, 23, 1129-1137.

Liljas, A., Ehrenberg, M., & Åqvist, J. (2011). Comment on “The mechanism for activation of GTP hydrolysis on the ribosome”. Science, 333, 37; author reply 37.

Ling, C., & Ermolenko, D.N. (2016). Structural insights into ribosome translocation. Wiley Interdiscip. Rev. RNA, 7, 620-636.

Liu, T., Kaplan, A., Alexander, L., Yan, S., Wen, J. Der, Lancaster, L., Wickersham, C.E., Fredrick, K., Fredrik, K., Noller, H., et al. (2014). Direct measurement of the mechanical work during translocation by the ribosome. Elife, 3, e03406.

Lodish, H.F. (1974). Model for the regulation of mRNA translation applied to haemoglobin synthesis. Nature, 251, 365-448.

Loerke, J., Giesebrecht, J., & Spahn, C.M.T. (2010). Multiparticle Cryo-EM of Ribosomes. Methods Enzymol., 483, 161-177.

Lomakin, I.B., & Steitz, T.A. (2013). The initiation of mammalian protein synthesis and mRNA scanning mechanism. Nature, 500, 307-311.

Mao, Y., Wang, L., Gu, C., Herschhorn, A., Désormeaux, A., Finzi, A., Xiang, S.-H., & Sodroski, J.G. (2013). Molecular architecture of the uncleaved HIV-1 envelope glycoprotein trimer. Proc. Natl. Acad. Sci. U.S.A., 110, 12438-12443.

Maracci, C., & Rodnina, M.V. (2016). Review: Translational GTPases. Biopolymers, 105, 463-475.

Marcotrigiano, J., Gingras, A.C., Sonenberg, N., & Burley, S.K. (1999). Cap-dependent translation initiation in eukaryotes is regulated by a molecular mimic of eIF4G. Mol. Cell, 3, 707-716.

Márquez, V., Wilson, D.N., Tate, W.P., Triana-Alonso, F., & Nierhaus, K.H. (2004). Maintaining the ribosomal reading frame: The influence of the E site during translational regulation of release factor 2. Cell, 118, 45-55.

Martin-Pérez, J., & Thomas, G. (1983). Ordered phosphorylation of 40S ribosomal protein S6 after serum stimulation of quiescent 3T3 cells. Proc. Natl. Acad. Sci. U. S. A., 80, 926-930.

Mastronarde, D.N. (2005). Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol., 152, 36-51.

Mazmanian, S.K., Liu, G., Ton-That, H., & Schneewind, O. (1999). Staphylococcus aureus sortase, an enzyme that anchors surface proteins to the cell wall. Science, 285, 760-763.

Meister, G. (2011). RNA biology: an introduction. Wiley-VCH.

Melnikov, S., Ben-Shem, A., Garreau de Loubresse, N., Jenner, L., Yusupova, G., & Yusupov, M. (2012). One core, two shells: bacterial and eukaryotic ribosomes. Nat. Struct. Mol. Biol., 19, 560-567.

Meyuhas, O. (2008). Chapter 1 Physiological Roles of Ribosomal Protein S6: One of Its Kind. Int. Rev. Cell Mol. Biol., 268, 1-37.

Meyuhas, O. (2015). Ribosomal Protein S6 Phosphorylation: Four Decades of Research. In International Review of Cell and Molecular Biology, (Elsevier Ltd), pp. 41-73.

Mieulet, V., Roceri, M., Espeillac, C., Sotiropoulos, A., Ohanna, M., Oorschot, V., Klumperman, J., Sandri, M., & Pende, M. (2007). S6 kinase inactivation impairs growth and translational target phosphorylation in muscle cells maintaining proper regulation of protein turnover. Am. J. Physiol. Physiol., 293, C712-C722.

Milon, P., Konevega, A.L., Gualerzi, C.O., & Rodnina, M.V. (2008). Kinetic checkpoint at a late step in translation initiation. Mol. Cell, 30, 712-720.

Mirande, M. (2010). Processivity of translation in the eukaryote cell: Role of aminoacyl-tRNA synthetases. FEBS Lett., 584, 443-447.

Mitchell, S.F., & Parker, R. (2014). Principles and Properties of Eukaryotic mRNPs. Mol. Cell, 54, 547-558.

Moazed, D., & Noller, H.F. (1989). Intermediate states in the movement of transfer RNA in the ribosome. Nature, 342, 142-148.

Mohan, S., & Noller, H.F. (2017). Recurring RNA structural motifs underlie the mechanics of L1 stalk movement. Nat. Commun., 8, 14285.

Munro, J.B., Altman, R.B., O’Connor, N., & Blanchard, S.C. (2007). Identification of Two Distinct Hybrid State Intermediates on the Ribosome. Mol. Cell, 25, 505-517.

Munro, J.B., Sanbonmatsu, K.Y., Spahn, C.M.T., & Blanchard, S.C. (2009). Navigating the ribosome’s metastable energy landscape. Trends Biochem. Sci., 34, 390-400.

Munro, J.B., Altman, R.B., Tung, C.-S., Sanbonmatsu, K.Y., & Blanchard, S.C. (2010). A fast dynamic mode of the EF-G-bound ribosome. EMBO J., 29, 770-781.

Murray, J., Savva, C.G., Shin, B.S., Dever, T.E., Ramakrishnan, V., & Fernández, I.S. (2016). Structural characterization of ribosome recruitment and translocation by type IV IRES. Elife, 5, e14690.

Myasnikov, A.G., Afonina, Z.A., Ménétret, J.-F., Shirokov, V.A., Spirin, A.S., & Klaholz, B.P. (2014). The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes. Nat. Commun., 5, 5294.

Nguyen, K., & Whitford, P.C. (2016). Steric interactions lead to collective tilting motion in the ribosome during mRNA-tRNA translocation. Nat. Commun., 7, 10586.

Nielsen, P.J., Duncan, R., & McConkey, E.H. (1981). Phosphorylation of Ribosomal Protein S6 Relationship to Protein Synthesis in HeLa Cells. Eur. J. Biochem., 120, 523-527.

Nierhaus, K.H. (1991). The assembly of prokaryotic ribosomes. Biochimie, 73, 739-755.

Nierhaus, K.H. (1993). Solution of the ribosome riddle: how the ribosome selects the correct aminoacyl-tRNA out of 41 similar contestants. Mol. Microbiol., 9, 661-669.

Nilsson, L., & Nygård, O. (1992). Reduced puromycin sensitivity of translocated polysomes after the addition of elongation factor 2 and non-hydrolysable GTP analogues. FEBS Lett., 309, 89-91.

Nissen, P., Hansen, J., Ban, N., Moore, P.B., & Steitz, T.A. (2000). The structural basis of ribosome activity in peptide bond synthesis. Science, 289, 920-930.

Ogle, J.M., Murphy IV, F.V., Tarry, M.J., & Ramakrishnan, V. (2002). Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell, 111, 721-732.

Oppenheimer, N.J., & Bodley, J.W. (1981). Diphtheria toxin. Site and configuration of ADP-ribosylation of diphthamide in elongation factor 2. J. Biol. Chem., 256, 8579-8581.

Orlova, E.V., & Saibil, H.R. (2011). Structural Analysis of Macromolecular Assemblies by Electron Microscopy. Chem. Rev., 111, 7710-7748.

Panić, L., Tamarut, S., Sticker-Jantscheff, M., Barkić, M., Solter, D., Uzelac, M., Grabusić, K., & Volarević, S. (2006). Ribosomal protein S6 gene haploinsufficiency is associated with activation of a p53-dependent checkpoint during gastrulation. Mol. Cell. Biol., 26, 8880-8891.

Pelletier, J., & Sonenberg, N. (1988). Internal initiation of translation of eukaryotic mRNA directed by a sequence derived from poliovirus RNA. Nature, 334, 320-325.

Penczek, P.A., Frank, J., & Spahn, C.M.T. (2006). A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation. J. Struct. Biol., 154, 184-194.

Pende, M., Um, S.H., Mieulet, V., Sticker, M., Goss, V.L., Mestan, J., Mueller, M., Fumagalli, S., Kozma, S.C., & Thomas, G. (2004). S6K1(-/-)/S6K2(-/-) mice exhibit perinatal lethality and rapamycin-sensitive 5’-terminal oligopyrimidine mRNA translation and reveal a mitogen-activated protein kinase-dependent S6 kinase pathway. Mol. Cell. Biol., 24, 3112-3124.

Pestova, T.V., & Hellen, C.U.T. (2003). Translation elongation after assembly of ribosomes on the Cricket paralysis virus internal ribosomal entry site without initiation factors or initiator tRNA. Genes Dev., 17, 181-186.

Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., & Ferrin, T.E. (2004). UCSF Chimera—A visualization system for exploratory research and analysis. J. Comput. Chem., 25, 1605-1612.

Pisarev, A.V., Skabkin, M.A., Pisareva, V.P., Skabkina, O.V., Rakotondrafara, A.M., Hentze, M.W., Hellen, C.U.T., & Pestova, T.V. (2010). The role of ABCE1 in eukaryotic posttermination ribosomal recycling. Mol. Cell, 37, 196-210.

Pulk, A., & Cate, J.H.D. (2013). Control of Ribosomal Subunit Rotation by Elongation Factor G. Science, 340, 1235970.

Punjani, A., Rubinstein, J.L., Fleet, D.J., & Brubaker, M.A. (2017). cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods, 14, 290-296.

Radon, J. (1986). On the determination of functions from their integral values along certain manifolds. IEEE Trans. Med. Imaging, 5, 170-176.

Ramesh, M., & Woolford, J.L. (2016). Eukaryote-specific rRNA expansion segments function in ribosome biogenesis. RNA, 22, 1153-1162.

Ramrath, D.J.F., Yamamoto, H., Rother, K., Wittek, D., Pech, M., Mielke, T., Loerke, J., Scheerer, P., Ivanov, P., Teraoka, Y., et al. (2012). The complex of tmRNA-SmpB and EF-G on translocating ribosomes. Nature, 485, 526-529.

Ramrath, D.J.F., Lancaster, L., Sprink, T., Mielke, T., Loerke, J., Noller, H.F., & Spahn, C.M.T. (2013). Visualization of two transfer RNAs trapped in transit during elongation factor G-mediated translocation. Proc. Natl. Acad. Sci., 110, 20964-20969.

Ramrath, D.J.F., Niemann, M., Leibundgut, M., Bieri, P., Prange, C., Horn, E.K., Leitner, A., Boehringer, D., Schneider, A., & Ban, N. (2018). Evolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes. Science, 362, eaau7735.

Ratje, A.H., Loerke, J., Mikolajka, A., Brünner, M., Hildebrand, P.W., Starosta, A.L., Dönhöfer, A., Connell, S.R., Fucini, P., Mielke, T., et al. (2010). Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites. Nature, 468, 713-716.

Reimer, L., & Kohl, H. (2008). Transmission electron microscopy: physics of image formation. Springer, 5th edition.

Rodnina, M.V., Savelsbergh, A., Katunin, V.I., & Wintermeyer, W. (1997). Hydrolysis of GTP by elongation factor G drives tRNA movement on the ribosome. Nature, 385, 37-41.

Rogg, H., Wehrli, W., & Staehelin, M. (1969). Isolation of mammalian transfer RNA. BBA Sect. Nucleic Acids Protein Synth., 195, 13-15.

Rohou, A., & Grigorieff, N. (2015). CTFFIND4: Fast and accurate defocus estimation from electron micrographs. J. Struct. Biol., 192, 216-221.

Rosenthal, P.B., & Henderson, R. (2003). Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol., 333, 721-745.

Roux, P.P., Shahbazian, D., Vu, H., Holz, M.K., Cohen, M.S., Taunton, J., Sonenberg, N., & Blenis, J. (2007). RAS/ERK Signaling Promotes Site-specific Ribosomal Protein S6 Phosphorylation via RSK and Stimulates Cap-dependent Translation. J. Biol. Chem., 282, 14056-14064.

Roy, A., Kucukural, A., & Zhang, Y. (2010). I-TASSER: a unified platform for automated protein structure and function prediction. Nat. Protoc., 5, 725-738.

Rubinstein, J.L., & Brubaker, M.A. (2015). Alignment of cryo-EM movies of individual particles by optimization of image translations. J. Struct. Biol., 192, 188-195.

Ruvinsky, I., Sharon, N., Lerer, T., Cohen, H., Stolovich-Rain, M., Nir, T., Dor, Y., Zisman, P., & Meyuhas, O. (2005). Ribosomal protein S6 phosphorylation is a determinant of cell size and glucose homeostasis. Genes Dev., 19, 2199-2211.

Ruvinsky, I., Katz, M., Dreazen, A., Gielchinsky, Y., Saada, A., Freedman, N., Mishani, E., Zimmerman, G., Kasir, J., & Meyuhas, O. (2009). Mice Deficient in Ribosomal Protein S6 Phosphorylation Suffer from Muscle Weakness that Reflects a Growth Defect and Energy Deficit. PLoS One, 4, e5618.

Scheres, S.H.W. (2012). RELION: Implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol., 180, 519-530.

Schmeing, T.M., & Ramakrishnan, V. (2009). What recent ribosome structures have revealed about the mechanism of translation. Nature, 461, 1234-1242.

Schuette, J.-C., Murphy, F.V., Kelley, A.C., Weir, J.R., Giesebrecht, J., Connell, S.R., Loerke, J., Mielke, T., Zhang, W., Penczek, P.A., et al. (2009). GTPase activation of elongation factor EF-Tu by the ribosome during decoding. EMBO J., 28, 755-765.

Schuwirth, B.S., Borovinskaya, M.A., Hau, C.W., Zhang, W., Vila-Sanjurjo, A., Holton, J.M., & Cate, J.H.D. (2005). Structures of the Bacterial Ribosome at 3.5 A Resolution. Science, 310, 827-834.

Schweins, T., Geyer, M., Scheffzek, K., Warshel, A., Kalbitzer, H.R., & Wittinghofer, A. (1995). Substrate-assisted catalysis as a mechanism for GTP hydrolysis of p21ras and other GTP-binding proteins. Nat. Struct. Biol., 2, 36-44.

Selmer, M., Dunham, C.M., Murphy, F.V., Weixlbaumer, A., Petry, S., Kelley, A.C., Weir, J.R., & Ramakrishnan, V. (2006). Structure of the 70S ribosome complexed with mRNA and tRNA. Science, 313, 1935-1942.

Semenkov, Y.P., Rodnina, M.V., & Wintermeyer, W. (1996). The “allosteric three-site model” of elongation cannot be confirmed in a well-defined ribosome system from Escherichia coli. Proc. Natl. Acad. Sci. U. S. A., 93, 12183-12188.

Shine, J., & Dalgarno, L. (1974). The 3’-Terminal Sequence of Escherichia coli 16S Ribosomal RNA: Complementarity to Nonsense Triplets and Ribosome Binding Sites. Proc. Natl. Acad. Sci., 71, 1342-1346.

Shirokikh, N.E., & Preiss, T. (2018). Translation initiation by cap-dependent ribosome recruitment: Recent insights and open questions. Wiley Interdiscip. Rev. RNA, 9, e1473.

Shirokikh, N.E., Archer, S.K., Beilharz, T.H., Powell, D., & Preiss, T. (2017). Translation complex profile sequencing to study the in vivo dynamics of mRNA-ribosome interactions during translation initiation, elongation and termination. Nat. Protoc., 12, 697-731.

Shoemaker, C.J., Eyler, D.E., & Green, R. (2010). Dom34:Hbs1 promotes subunit dissociation and peptidyl-tRNA drop-off to initiate no-go decay. Science, 330, 369-372.

Shoji, S., Walker, S.E., & Fredrick, K. (2009). Ribosomal Translocation: One Step Closer to the Molecular Mechanism. ACS Chem. Biol., 4, 93-107.

Simonetti, A., Marzi, S., Myasnikov, A.G., Fabbretti, A., Yusupov, M., Gualerzi, C.O., & Klaholz, B.P. (2008). Structure of the 30S translation initiation complex. Nature, 455, 416-420.

Skabkin, M.A., Skabkina, O.V., Hellen, C.U.T., & Pestova, T.V. (2013). Reinitiation and other unconventional posttermination events during eukaryotic translation. Mol. Cell, 51, 249-264.

Spahn, C.M., Penczek, P.A., Leith, A., & Frank, J. (2000). A method for differentiating proteins from nucleic acids in intermediate-resolution density maps: cryo-electron microscopy defines the quaternary structure of the Escherichia coli 70S ribosome. Structure, 8, 937-948.

Spahn, C.M., Gomez-Lorenzo, M.G., Grassucci, R.A., Jørgensen, R., Andersen, G.R., Beckmann, R., Penczek, P.A., Ballesta, J.P., & Frank, J. (2004). Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation. EMBO J., 23, 1008-1019.

Spahn, C.M.T., Jan, E., Mulder, A., Grassucci, R.A., Sarnow, P., & Frank, J. (2004). Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: the IRES functions as an RNA-based translation factor. Cell, 118, 465-475.

Spirin, A.S. (2009). The Ribosome as a Conveying Thermal Ratchet Machine. J. Biol. Chem., 284, 21103-21119.

Stapulionis, R., & Deutscher, M.P. (1995). A channeled tRNA cycle during mammalian protein synthesis. Proc. Natl. Acad. Sci. U. S. A., 92, 7158-7161.

Sulić, S., Panić, L., Barkić, M., Merćep, M., Uzelac, M., & Volarević, S. (2005). Inactivation of S6 ribosomal protein gene in T lymphocytes activates a p53-dependent checkpoint response. Genes Dev., 19, 3070-3082.

Susorov, D., Zakharov, N., Shuvalova, E., Ivanov, A., Egorova, T., Shuvalov, A., Shatsky, I.N., & Alkalaeva, E. (2018). Eukaryotic translation elongation factor 2 (eEF2) catalyzes reverse translocation of the eukaryotic ribosome. J. Biol. Chem., 293, 5220-5229.

Tang, G., Peng, L., Baldwin, P.R., Mann, D.S., Jiang, W., Rees, I., & Ludtke, S.J. (2007). EMAN2: An extensible image processing suite for electron microscopy. J. Struct. Biol., 157, 38-46.

Tourigny, D.S., Fernandez, I.S., Kelley, A.C., & Ramakrishnan, V. (2013). Elongation factor G bound to the ribosome in an intermediate state of translocation. Science, 340, 1235490.

Triana, F., Nierhaus, K.H., & Chakraburtty, K. (1994). Transfer RNA binding to 80S ribosomes from yeast: evidence for three sites. Biochem Mol Biol Int., 33, 909-915.

Tsuboi, T., Kuroha, K., Kudo, K., Makino, S., Inoue, E., Kashima, I., & Inada, T. (2012). Dom34:Hbs1 Plays a General Role in Quality-Control Systems by Dissociation of a Stalled Ribosome at the 3′ End of Aberrant mRNA. Mol. Cell, 46, 518-529.

UniProt Consortium, T.U. (2008). The universal protein resource (UniProt). Nucleic Acids Res., 36, D190-D195.

Valle, M., Zavialov, A., Sengupta, J., Rawat, U., Ehrenberg, M., & Frank, J. (2003). Locking and unlocking of ribosomal motions. Cell, 114, 123-134.

Viero, G., Lunelli, L., Passerini, A., Bianchini, P., Gilbert, R.J., Bernabò, P., Tebaldi, T., Diaspro, A., Pederzolli, C., & Quattrone, A. (2015). Three distinct ribosome assemblies modulated by translation are the building blocks of polysomes. J. Cell Biol., 208, 581-596.

Volarevic, S. (2000). Proliferation, But Not Growth, Blocked by Conditional Deletion of 40S Ribosomal Protein S6. Science, 288, 2045-2047.

Voorhees, R.M., Schmeing, T.M., Kelley, A.C., & Ramakrishnan, V. (2010). The Mechanism for Activation of GTP Hydrolysis on the Ribosome. Science, 330, 835-838.

Voorhees, R.M., Fernández, I.S., Scheres, S.H.W., & Hegde, R.S. (2014). Structure of the Mammalian Ribosome-Sec61 Complex to 3.4 Å Resolution. Cell, 157, 1632-1643.

Wasserman, M.R., Alejo, J.L., Altman, R.B., & Blanchard, S.C. (2016). Multiperspective smFRET reveals rate-determining late intermediates of ribosomal translocation. Nat. Struct. Mol. Biol., 23, 333-341.

Wettenhall, R.E.H., & Morgan, F.J. (1984). Phosphorylation of hepatic ribosomal protein S6 and 80 and 40 S ribosomes. Primary structure of S6 in the region of the major phosphorylation sites for cAMP-dependent protein kinases. J. Biol. Chem., 259, 2084-2091.

Wettenhall, R.E.H., Erikson, E., & Maller, J.L. (1992). Ordered multisite phosphorylation of Xenopus ribosomal protein S6 by S6 kinase II. J. Biol. Chem., 267, 9021-9027.

Whitford, P.C., Ahmed, A., Yu, Y., Hennelly, S.P., Tama, F., Spahn, C.M.T., Onuchic, J.N., & Sanbonmatsu, K.Y. (2011). Excited states of ribosome translocation revealed through integrative molecular modeling. Proc. Natl. Acad. Sci. U. S. A., 108, 18943-18948.

Wilson, D.N., & Nierhaus, K.H. (2007). The Weird and Wonderful World of Bacterial Ribosome Regulation. Crit. Rev. Biochem. Mol. Biol., 42, 187-219.

Wittinghofer, A., & Vetter, I.R. (2011). Structure-Function Relationships of the G Domain, a Canonical Switch Motif. Annu. Rev. Biochem., 80, 943-971.

Wool, I.G. (1979). The Structure and Function of Eukaryotic Ribosomes. Annu. Rev. Biochem., 48, 719-754.

Xue, S., & Barna, M. (2012). Specialized ribosomes: a new frontier in gene regulation and organismal biology. Nat. Rev. Mol. Cell Biol., 13, 355-369.

Yamamoto, H., Unbehaun, A., & Spahn, C.M.T. (2017). Ribosomal Chamber Music: Toward an Understanding of IRES Mechanisms. Trends Biochem. Sci., 42, 655-668.

Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., & Zhang, Y. (2015). The I-TASSER Suite: protein structure and function prediction. Nat. Methods, 12, 7-8.

Yusupova, G., & Yusupov, M. (2017). Crystal structure of eukaryotic ribosome and its complexes with inhibitors. Philos. Trans. R. Soc. B Biol. Sci., 372, 20160184.

Zernike, F. (1942). Phase contrast, a new method for the microscopic observation of transparent objects, Part I. Physica, 9, 974-986.

Zhang, K. (2016). Gctf: Real-time CTF determination and correction. J. Struct. Biol., 193, 1-12.

Zheng, S.Q., Palovcak, E., Armache, J.-P., Verba, K.A., Cheng, Y., & Agard, D.A. (2017). MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods, 14, 331-332.

Zhou, J., Lancaster, L., Donohue, J.P., & Noller, H.F. (2013). Crystal Structures of EF-G – Ribosome States of Translocation. Science, 340, 1235490.

Zhou, J., Lancaster, L., Donohue, J.P., & Noller, H.F. (2014). How the ribosome hands the A-site tRNA to the P site during EF-G-catalyzed translocation. Science, 345, 1188-1191.