High-resolution structure of the Escherichia coli ribosome

Noeske, Jonas; Wasserman, Michael R.; Terry, Daniel S.; Altman, Roger B.; Blanchard, Scott C.; Cate, Jamie H. D.

doi:10.1038/nsmb.2994

Title: High-resolution structure of the Escherichia coli ribosome

Journal Article · Mon Mar 16 00:00:00 EDT 2015 · Nature Structural & Molecular Biology

DOI:https://doi.org/10.1038/nsmb.2994· OSTI ID:1347117

Noeske, Jonas ^[1]; Wasserman, Michael R. ^[2]; Terry, Daniel S. ^[2]; Altman, Roger B. ^[2]; Blanchard, Scott C. ^[3]; Cate, Jamie H. D. ^[1]

Univ. of California, Berkeley, CA (United States)
Weill Cornell Medical College, New York, NY (United States)
Weill Cornell Medical College, New York, NY (United States); Rockefeller Univ., New York, NY (United States)

Protein synthesis by the ribosome is highly dependent on the ionic conditions in the cellular environment, but the roles of ribosome solvation remain poorly understood. Moreover, the function of modifications to ribosomal RNA and ribosomal proteins are unclear. Here we present the structure of the Escherichia coli 70S ribosome to 2.4 Å resolution. The structure reveals details of the ribosomal subunit interface that are conserved in all domains of life, and suggest how solvation contributes to ribosome integrity and function. The structure also suggests how the conformation of ribosomal protein uS12 likely impacts its contribution to messenger RNA decoding. In conclusion, this structure helps to explain the phylogenetic conservation of key elements of the ribosome, including posttranscriptional and posttranslational modifications and should serve as a basis for future antibiotic development.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: University of California, Berkeley, CA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1347117

Journal Information:: Nature Structural & Molecular Biology, Vol. 22, Issue 4; ISSN 1545-9993

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 160 works

Citation information provided by
Web of Science

References (82)

Nucleoside triphosphate regeneration decreases the frequency of translation errors. Jelenc, P. C.; Kurland, C. G. Proceedings of the National Academy of Sciences, Vol. 76, Issue 7 https://doi.org/10.1073/pnas.76.7.3174	journal	July 1979
Fluctuations of Transfer RNAs between Classical and Hybrid States Kim, Harold D.; Puglisi, Joseph D.; Chu, Steven Biophysical Journal, Vol. 93, Issue 10 https://doi.org/10.1529/biophysj.107.109884	journal	November 2007
Optimization of speed and accuracy of decoding in translation Wohlgemuth, Ingo; Pohl, Corinna; Rodnina, Marina V. The EMBO Journal, Vol. 29, Issue 21 https://doi.org/10.1038/emboj.2010.229	journal	September 2010
Erratum: Aminoglycoside activity observed on single pre-translocation ribosome complexes Feldman, Michael B.; Terry, Daniel S.; Altman, Roger B. Nature Chemical Biology, Vol. 6, Issue 3 https://doi.org/10.1038/nchembio0310-244c	journal	March 2010
Correlated conformational events in EF-G and the ribosome regulate translocation Munro, James B.; Wasserman, Michael R.; Altman, Roger B. Nature Structural & Molecular Biology, Vol. 17, Issue 12 https://doi.org/10.1038/nsmb.1925	journal	November 2010
Solvent-accessible surfaces of nucleic acids Alden, Charles J.; Kim, Sung-Hou Journal of Molecular Biology, Vol. 132, Issue 3 https://doi.org/10.1016/0022-2836(79)90268-7	journal	August 1979
The RNA Modification Database: 1999 update Rozenski, J.; Crain, P. F.; McCloskey, J. A. Nucleic Acids Research, Vol. 27, Issue 1 https://doi.org/10.1093/nar/27.1.196	journal	January 1999
Expanding the Nucleotide Repertoire of the Ribosome with Post-Transcriptional Modifications Chow, Christine S.; Lamichhane, Tek N.; Mahto, Santosh K. ACS Chemical Biology, Vol. 2, Issue 9 https://doi.org/10.1021/cb7001494	journal	September 2007
The Importance of Being Modified: Roles of Modified Nucleosides and Mg2+ in RNA Structure and Function Agris, Paul F. Progress in Nucleic Acid Research and Molecular Biology https://doi.org/10.1016/S0079-6603(08)60143-9	book	January 1996
Predicting the Minimal Translation Apparatus: Lessons from the Reductive Evolution of Mollicutes Grosjean, Henri; Breton, Marc; Sirand-Pugnet, Pascal PLoS Genetics, Vol. 10, Issue 5 https://doi.org/10.1371/journal.pgen.1004363	journal	May 2014
The pseudouridine synthase RluD is required for normal ribosome assembly and function in Escherichia coli Gutgsell, N. S. RNA, Vol. 11, Issue 7 https://doi.org/10.1261/rna.2550105	journal	July 2005
Pseudouridylation of helix 69 of 23S rRNA is necessary for an effective translation termination Ejby, M.; Sorensen, M. A.; Pedersen, S. Proceedings of the National Academy of Sciences, Vol. 104, Issue 49 https://doi.org/10.1073/pnas.0706558104	journal	November 2007
Identification and characterization of RsmE, the founding member of a new RNA base methyltransferase family Basturea, G. N. RNA, Vol. 12, Issue 3 https://doi.org/10.1261/rna.2283106	journal	March 2006
YgdE is the 2′- O- ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA Purta, Elzbieta; O'Connor, Michelle; Bujnicki, Janusz M. Molecular Microbiology, Vol. 72, Issue 5 https://doi.org/10.1111/j.1365-2958.2009.06709.x	journal	June 2009
Sudestada1, a Drosophila ribosomal prolyl-hydroxylase required for mRNA translation, cell homeostasis, and organ growth Katz, M. J.; Acevedo, J. M.; Loenarz, C. Proceedings of the National Academy of Sciences, Vol. 111, Issue 11 https://doi.org/10.1073/pnas.1314485111	journal	February 2014
Hydroxylation of the eukaryotic ribosomal decoding center affects translational accuracy Loenarz, C.; Sekirnik, R.; Thalhammer, A. Proceedings of the National Academy of Sciences, Vol. 111, Issue 11 https://doi.org/10.1073/pnas.1311750111	journal	February 2014
OGFOD1 catalyzes prolyl hydroxylation of RPS23 and is involved in translation control and stress granule formation Singleton, R. S.; Liu-Yi, P.; Formenti, F. Proceedings of the National Academy of Sciences, Vol. 111, Issue 11 https://doi.org/10.1073/pnas.1314482111	journal	February 2014
How Should We Think About the Ribosome? Moore, Peter B. Annual Review of Biophysics, Vol. 41, Issue 1 https://doi.org/10.1146/annurev-biophys-050511-102314	journal	June 2012
A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome Polikanov, Yury S.; Steitz, Thomas A.; Innis, C. Axel Nature Structural & Molecular Biology, Vol. 21, Issue 9 https://doi.org/10.1038/nsmb.2871	journal	August 2014
Amicoumacin A Inhibits Translation by Stabilizing mRNA Interaction with the Ribosome Polikanov, Yury S.; Osterman, Ilya A.; Szal, Teresa Molecular Cell, Vol. 56, Issue 4 https://doi.org/10.1016/j.molcel.2014.09.020	journal	November 2014
Structures of the Ribosome in Intermediate States of Ratcheting Zhang, W.; Dunkle, J. A.; Cate, J. H. D. Science, Vol. 325, Issue 5943, p. 1014-1017 https://doi.org/10.1126/science.1175275	journal	August 2009
Linking Crystallographic Model and Data Quality Karplus, P. A.; Diederichs, K. Science, Vol. 336, Issue 6084 https://doi.org/10.1126/science.1218231	journal	May 2012
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
Posttranslational Modifications of Ribosomal Proteins in Escherichia coli Nesterchuk, M. V.; Sergiev, P. V.; Dontsova, O. A. Acta Naturae, Vol. 3, Issue 2 https://doi.org/10.32607/20758251-2011-3-2-22-33	journal	June 2011
Oxygenase-catalyzed ribosome hydroxylation occurs in prokaryotes and humans Ge, Wei; Wolf, Alexander; Feng, Tianshu Nature Chemical Biology, Vol. 8, Issue 12 https://doi.org/10.1038/nchembio.1093	journal	October 2012
A novel partial modification at C2501 in Escherichia coli 23S ribosomal RNA Andersen, T. E. RNA, Vol. 10, Issue 6 https://doi.org/10.1261/rna.5259404	journal	June 2004
Effect of polyamines on translation fidelity in vivo McMURRY, Laura M.; Algranati, Israel D. European Journal of Biochemistry, Vol. 155, Issue 2 https://doi.org/10.1111/j.1432-1033.1986.tb09502.x	journal	March 1986
tRNA dynamics on the ribosome during translation Blanchard, S. C.; Kim, H. D.; Gonzalez, R. L. Proceedings of the National Academy of Sciences, Vol. 101, Issue 35, p. 12893-12898 https://doi.org/10.1073/pnas.0403884101	journal	August 2004
tRNA selection and kinetic proofreading in translation Blanchard, Scott C.; Gonzalez, Ruben L.; Kim, Harold D. Nature Structural & Molecular Biology, Vol. 11, Issue 10 https://doi.org/10.1038/nsmb831	journal	September 2004
A guide to ions and RNA structure Draper, D. E. RNA, Vol. 10, Issue 3 https://doi.org/10.1261/rna.5205404	journal	March 2004
Structures of the Bacterial Ribosome at 3.5 Å Resolution Schuwirth, Barbara S.; Borovinskaya, Maria A.; Hau, Cathy W. Science, Vol. 310, Issue 5749 https://doi.org/10.1126/science.1117230	journal	November 2005
Structures of the Bacterial Ribosome in Classical and Hybrid States of tRNA Binding Dunkle, J. A.; Wang, L.; Feldman, M. B. Science, Vol. 332, Issue 6032 https://doi.org/10.1126/science.1202692	journal	May 2011
RNA tertiary interactions in the large ribosomal subunit: The A-minor motif Nissen, P.; Ippolito, J. A.; Ban, N. Proceedings of the National Academy of Sciences, Vol. 98, Issue 9 https://doi.org/10.1073/pnas.081082398	journal	April 2001
The Structure of the Eukaryotic Ribosome at 3.0 A Resolution Ben-Shem, A.; Garreau de Loubresse, N.; Melnikov, S. Science, Vol. 334, Issue 6062 https://doi.org/10.1126/science.1212642	journal	November 2011
Selective Protein Synthesis by Ribosomes with a Drug-Obstructed Exit Tunnel Kannan, Krishna; Vázquez-Laslop, Nora; Mankin, Alexander S. Cell, Vol. 151, Issue 3 https://doi.org/10.1016/j.cell.2012.09.018	journal	October 2012
Macrolide antibiotics allosterically predispose the ribosome for translation arrest Sothiselvam, Shanmugapriya; Liu, Bo; Han, Wei Proceedings of the National Academy of Sciences, Vol. 111, Issue 27 https://doi.org/10.1073/pnas.1403586111	journal	June 2014
Revisiting the structures of several antibiotics bound to the bacterial ribosome Bulkley, D.; Innis, C. A.; Blaha, G. Proceedings of the National Academy of Sciences, Vol. 107, Issue 40 https://doi.org/10.1073/pnas.1008685107	journal	September 2010
Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action Dunkle, J. A.; Xiong, L.; Mankin, A. S. Proceedings of the National Academy of Sciences, Vol. 107, Issue 40 https://doi.org/10.1073/pnas.1007988107	journal	September 2010
The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 A Resolution Ban, N. Science, Vol. 289, Issue 5481 https://doi.org/10.1126/science.289.5481.905	journal	August 2000
High Resolution Structure of the Large Ribosomal Subunit from a Mesophilic Eubacterium Harms, Joerg; Schluenzen, Frank; Zarivach, Raz Cell, Vol. 107, Issue 5 https://doi.org/10.1016/S0092-8674(01)00546-3	journal	November 2001
SecM-Stalled Ribosomes Adopt an Altered Geometry at the Peptidyl Transferase Center Bhushan, Shashi; Hoffmann, Thomas; Seidelt, Birgit PLoS Biology, Vol. 9, Issue 1 https://doi.org/10.1371/journal.pbio.1000581	journal	January 2011
Mechanisms of SecM-Mediated Stalling in the Ribosome Gumbart, James; Schreiner, Eduard; Wilson, Daniel N. Biophysical Journal, Vol. 103, Issue 2 https://doi.org/10.1016/j.bpj.2012.06.005	journal	July 2012
Molecular Basis for the Ribosome Functioning as an L-Tryptophan Sensor Bischoff, Lukas; Berninghausen, Otto; Beckmann, Roland Cell Reports, Vol. 9, Issue 2 https://doi.org/10.1016/j.celrep.2014.09.011	journal	October 2014
Structural Basis for Translational Stalling by Human Cytomegalovirus and Fungal Arginine Attenuator Peptide Bhushan, Shashi; Meyer, Helge; Starosta, Agata L. Molecular Cell, Vol. 40, Issue 1 https://doi.org/10.1016/j.molcel.2010.09.009	journal	October 2010
Crucial elements that maintain the interactions between the regulatory TnaC peptide and the ribosome exit tunnel responsible for Trp inhibition of ribosome function Martínez, Allyson K.; Shirole, Nitin H.; Murakami, Shino Nucleic Acids Research, Vol. 40, Issue 5 https://doi.org/10.1093/nar/gkr1052	journal	November 2011
Structure of the 70S Ribosome Complexed with mRNA and tRNA Selmer, M. Science, Vol. 313, Issue 5795 https://doi.org/10.1126/science.1131127	journal	September 2006
Conformational rigidity of specific pyrimidine residues in tRNA arises from posttranscriptional modifications that enhance steric interaction between the base and the 2'-hydroxyl group Kawai, Gota; Yamamoto, Yuriko; Kamimura, Takashi Biochemistry, Vol. 31, Issue 4 https://doi.org/10.1021/bi00119a012	journal	February 1992
Conformational flexibility in RNA: the role of dihydrouridine Dalluge, J. Nucleic Acids Research, Vol. 24, Issue 6 https://doi.org/10.1093/nar/24.6.1073	journal	March 1996
Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information Song, Jiangning; Burrage, Kevin; Yuan, Zheng BMC Bioinformatics, Vol. 7, Issue 1 https://doi.org/10.1186/1471-2105-7-124	journal	March 2006
A Proteomic and Transcriptomic Approach Reveals New Insight into β-methylthiolation of Escherichia coli Ribosomal Protein S12 Strader, Michael Brad; Costantino, Nina; Elkins, Christopher A. Molecular & Cellular Proteomics, Vol. 10, Issue 3 https://doi.org/10.1074/mcp.M110.005199	journal	December 2010
RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli Anton, B. P.; Saleh, L.; Benner, J. S. Proceedings of the National Academy of Sciences, Vol. 105, Issue 6 https://doi.org/10.1073/pnas.0708608105	journal	February 2008
Prevalence of syn nucleobases in the active sites of functional RNAs Sokoloski, J. E.; Godfrey, S. A.; Dombrowski, S. E. RNA, Vol. 17, Issue 10 https://doi.org/10.1261/rna.2759911	journal	August 2011
How the ribosome hands the A-site tRNA to the P site during EF-G-catalyzed translocation Zhou, J.; Lancaster, L.; Donohue, J. P. Science, Vol. 345, Issue 6201 https://doi.org/10.1126/science.1255030	journal	September 2014
Structural Insights into the Roles of Water and the 2′ Hydroxyl of the P Site tRNA in the Peptidyl Transferase Reaction Schmeing, T. Martin; Huang, Kevin S.; Kitchen, David E. Molecular Cell, Vol. 20, Issue 3 https://doi.org/10.1016/j.molcel.2005.09.006	journal	November 2005
Revisiting the Haloarcula marismortui 50S ribosomal subunit model Gabdulkhakov, Azat; Nikonov, Stanislav; Garber, Maria Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 6 https://doi.org/10.1107/S0907444913004745	journal	May 2013
Ordered water in macromolecular structure Karplus, P. Andrew; Faerman, Carlos Current Opinion in Structural Biology, Vol. 4, Issue 5 https://doi.org/10.1016/S0959-440X(94)90178-3	journal	October 1994
Structural aspects of messenger RNA reading frame maintenance by the ribosome Jenner, Lasse B.; Demeshkina, Natalia; Yusupova, Gulnara Nature Structural & Molecular Biology, Vol. 17, Issue 5 https://doi.org/10.1038/nsmb.1790	journal	April 2010
Allosteric control of the ribosome by small-molecule antibiotics Wang, Leyi; Pulk, Arto; Wasserman, Michael R. Nature Structural & Molecular Biology, Vol. 19, Issue 9 https://doi.org/10.1038/nsmb.2360	journal	August 2012
Identification of Two Distinct Hybrid State Intermediates on the Ribosome Munro, James B.; Altman, Roger B.; O'Connor, Nathan Molecular Cell, Vol. 25, Issue 4, p. 505-517 https://doi.org/10.1016/j.molcel.2007.01.022	journal	February 2007
An Oxygen Scavenging System for Improvement of Dye Stability in Single-Molecule Fluorescence Experiments Aitken, Colin Echeverría; Marshall, R. Andrew; Puglisi, Joseph D. Biophysical Journal, Vol. 94, Issue 5 https://doi.org/10.1529/biophysj.107.117689	journal	March 2008
Mitigating Unwanted Photophysical Processes for Improved Single-Molecule Fluorescence Imaging Dave, Richa; Terry, Daniel S.; Munro, James B. Biophysical Journal, Vol. 96, Issue 6 https://doi.org/10.1016/j.bpj.2008.11.061	journal	March 2009
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
The use of Sayre's equation with solvent flattening and histogram matching for phase extension and refinement of protein structures Zhang, K. Y. J.; Main, P. Acta Crystallographica Section A Foundations of Crystallography, Vol. 46, Issue 5 https://doi.org/10.1107/S0108767389012158	journal	May 1990
A Detailed View of a Ribosomal Active Site Wimberly, Brian T.; Guymon, Rebecca; McCutcheon, John P. Cell, Vol. 97, Issue 4 https://doi.org/10.1016/S0092-8674(00)80759-X	journal	May 1999
Energetically significant networks of coupled interactions within an unfolded protein Cho, J. -H.; Meng, W.; Sato, S. Proceedings of the National Academy of Sciences, Vol. 111, Issue 33 https://doi.org/10.1073/pnas.1402054111	journal	August 2014
Structural basis for the interaction of protein S1 with the Escherichia coli ribosome Byrgazov, Konstantin; Grishkovskaya, Irina; Arenz, Stefan Nucleic Acids Research, Vol. 43, Issue 1 https://doi.org/10.1093/nar/gku1314	journal	December 2014
A Compact Viral Processing Proteinase/Ubiquitin Hydrolase from the OTU Family Lombardi, Charlotte; Ayach, Maya; Beaurepaire, Lionel PLoS Pathogens, Vol. 9, Issue 8 https://doi.org/10.1371/journal.ppat.1003560	journal	August 2013
Extreme Temperature Tolerance of a Hyperthermophilic Protein Coupled to Residual Structure in the Unfolded State Wallgren, Marcus; Ådén, Jörgen; Pylypenko, Olena Journal of Molecular Biology, Vol. 379, Issue 4 https://doi.org/10.1016/j.jmb.2008.04.007	journal	June 2008
Structural and Functional Analysis of the E. coli NusB-S10 Transcription Antitermination Complex Luo, Xiao; Hsiao, He-Hsuan; Bubunenko, Mikhail Molecular Cell, Vol. 32, Issue 6 https://doi.org/10.1016/j.molcel.2008.10.028	journal	December 2008
FEM: feature-enhanced map Afonine, Pavel V.; Moriarty, Nigel W.; Mustyakimov, Marat Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 3 https://doi.org/10.1107/S1399004714028132	journal	February 2015
The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs Cannone, Jamie J.; Subramanian, Sankar; Schnare, Murray N. BMC Bioinformatics, Vol. 3, Issue 1 https://doi.org/10.1186/1471-2105-3-2	journal	January 2002
Temperature-sensitive mutations demonstrate roles for yeast fibrillarin in pre-rRNA processing, pre-rRNA methylation, and ribosome assembly Tollervey, David; Lehtonen, Hanna; Jansen, Ralf Cell, Vol. 72, Issue 3 https://doi.org/10.1016/0092-8674(93)90120-f	journal	February 1993
Restoration of Single-Channel Currents Using the Segmental k-Means Method Based on Hidden Markov Modeling Qin, Feng Biophysical Journal, Vol. 86, Issue 3 https://doi.org/10.1016/s0006-3495(04)74217-4	journal	March 2004
Ribosomal Mechanics, Antibiotics, and GTP Hydrolysis Porse, Bo T.; Garrett, Roger A. Cell, Vol. 97, Issue 4 https://doi.org/10.1016/s0092-8674(00)80751-5	journal	May 1999
Designer drugs for discerning bugs Douthwaite, Stephen Proceedings of the National Academy of Sciences, Vol. 107, Issue 40 https://doi.org/10.1073/pnas.1012547107	journal	September 2010
Least-squares phase refinement. II. High-resolution phasing of a small protein Sayre, D. Acta Crystallographica Section A, Vol. 30, Issue 2 https://doi.org/10.1107/s0567739474000404	journal	March 1974
Synergy of Streptogramin Antibiotics Occurs Independently of Their Effects on Translation Noeske, Jonas; Huang, Jian; Olivier, Nelson B. Antimicrobial Agents and Chemotherapy, Vol. 58, Issue 9 https://doi.org/10.1128/aac.03389-14	journal	June 2014
Inactivation of the RluD Pseudouridine Synthase Has Minimal Effects on Growth and Ribosome Function in Wild-Type Escherichia coli and Salmonella enterica O'Connor, M.; Gregory, S. T. Journal of Bacteriology, Vol. 193, Issue 1 https://doi.org/10.1128/jb.00970-10	journal	October 2010
Resistance to Macrolide, Lincosamide, Streptogramin, Ketolide, and Oxazolidinone Antibiotics Roberts, Marilyn C. Molecular Biotechnology, Vol. 28, Issue 1 https://doi.org/10.1385/mb:28:1:47	journal	January 2004

Cited By (60)

Mirror‐Image 5S Ribonucleoprotein Complexes Ling, Jun‐Jie; Fan, Chuyao; Qin, Hong Angewandte Chemie, Vol. 132, Issue 9 https://doi.org/10.1002/ange.201914799	journal	January 2020
Mirror‐Image 5S Ribonucleoprotein Complexes Ling, Jun‐Jie; Fan, Chuyao; Qin, Hong Angewandte Chemie International Edition, Vol. 59, Issue 9 https://doi.org/10.1002/anie.201914799	journal	January 2020
Defects in the Assembly of Ribosomes Selected for β-Amino Acid Incorporation Ward, Fred R.; Watson, Zoe L.; Ad, Omer Biochemistry, Vol. 58, Issue 45 https://doi.org/10.1021/acs.biochem.9b00746	journal	October 2019
Ribosome-dependent activation of stringent control Brown, Alan; Fernández, Israel S.; Gordiyenko, Yuliya Nature, Vol. 534, Issue 7606 https://doi.org/10.1038/nature17675	journal	May 2016
Mechanistic insights into the alternative translation termination by ArfA and RF2 Ma, Chengying; Kurita, Daisuke; Li, Ningning Nature, Vol. 541, Issue 7638 https://doi.org/10.1038/nature20822	journal	December 2016
Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome Zeng, Fuxing; Chen, Yanbo; Remis, Jonathan Nature, Vol. 541, Issue 7638 https://doi.org/10.1038/nature21053	journal	January 2017
Structural and evolutionary insights into ribosomal RNA methylation Sergiev, Petr V.; Aleksashin, Nikolay A.; Chugunova, Anastasia A. Nature Chemical Biology, Vol. 14, Issue 3 https://doi.org/10.1038/nchembio.2569	journal	February 2018
Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon Jomaa, Ahmad; Boehringer, Daniel; Leibundgut, Marc Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms10471	journal	January 2016
The signal recognition particle contacts uL23 and scans substrate translation inside the ribosomal tunnel Denks, Kärt; Sliwinski, Nadine; Erichsen, Veronika Nature Microbiology, Vol. 2, Issue 4 https://doi.org/10.1038/nmicrobiol.2016.265	journal	January 2017
A general mechanism of ribosome dimerization revealed by single-particle cryo-electron microscopy Franken, Linda E.; Oostergetel, Gert T.; Pijning, Tjaard Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-00718-x	journal	September 2017
Dissecting ribosomal particles throughout the kingdoms of life using advanced hybrid mass spectrometry methods van de Waterbeemd, Michiel; Tamara, Sem; Fort, Kyle L. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-04853-x	journal	June 2018
Structure of ribosome-bound azole-modified peptide phazolicin rationalizes its species-specific mode of bacterial translation inhibition Travin, Dmitrii Y.; Watson, Zoe L.; Metelev, Mikhail Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-12589-5	journal	October 2019
Small is big in Arabidopsis mitochondrial ribosome Waltz, Florent; Nguyen, Tan-Trung; Arrivé, Mathilde Nature Plants, Vol. 5, Issue 1 https://doi.org/10.1038/s41477-018-0339-y	journal	January 2019
De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes Kappel, Kalli; Liu, Shiheng; Larsen, Kevin P. Nature Methods, Vol. 15, Issue 11 https://doi.org/10.1038/s41592-018-0172-2	journal	October 2018
Structural basis for selective stalling of human ribosome nascent chain complexes by a drug-like molecule Li, Wenfei; Ward, Fred R.; McClure, Kim F. Nature Structural & Molecular Biology, Vol. 26, Issue 6 https://doi.org/10.1038/s41594-019-0236-8	journal	June 2019
Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF, tmRNA, and P-tRNA Mishra, Satabdi; Ahmed, Tofayel; Tyagi, Anu Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-31850-3	journal	September 2018
Structural basis of translation inhibition by cadazolid, a novel quinoxolidinone antibiotic Scaiola, Alain; Leibundgut, Marc; Boehringer, Daniel Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-42155-4	journal	April 2019
Amicoumacin A induces cancer cell death by targeting the eukaryotic ribosome Prokhorova, Irina V.; Akulich, Kseniya A.; Makeeva, Desislava S. Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep27720	journal	June 2016
Cryo-EM structure of the large subunit of the spinach chloroplast ribosome Ahmed, Tofayel; Yin, Zhan; Bhushan, Shashi Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep35793	journal	October 2016
Single methylation of 23S rRNA triggers late steps of 50S ribosomal subunit assembly Arai, Taiga; Ishiguro, Kensuke; Kimura, Satoshi Proceedings of the National Academy of Sciences, Vol. 112, Issue 34 https://doi.org/10.1073/pnas.1506749112	journal	August 2015
Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus Eyal, Zohar; Matzov, Donna; Krupkin, Miri Proceedings of the National Academy of Sciences, Vol. 112, Issue 43 https://doi.org/10.1073/pnas.1517952112	journal	October 2015
Structures of the orthosomycin antibiotics avilamycin and evernimicin in complex with the bacterial 70S ribosome Arenz, Stefan; Juette, Manuel F.; Graf, Michael Proceedings of the National Academy of Sciences, Vol. 113, Issue 27 https://doi.org/10.1073/pnas.1604790113	journal	June 2016
Mechanism of premature translation termination on a sense codon Svidritskiy, Egor; Demo, Gabriel; Korostelev, Andrei A. Journal of Biological Chemistry, Vol. 293, Issue 32 https://doi.org/10.1074/jbc.aw118.003232	journal	June 2018
A two-step probing method to compare lysine accessibility across macromolecular complex conformations MacRae, Andrew J.; Coltri, Patricia; Hrabeta-Robinson, Eva RNA Biology, Vol. 16, Issue 10 https://doi.org/10.1080/15476286.2019.1632777	journal	June 2019
Mutational characterization and mapping of the 70S ribosome active site d’Aquino, Anne E.; Azim, Tasfia; Aleksashin, Nikolay A. Nucleic Acids Research, Vol. 48, Issue 5 https://doi.org/10.1093/nar/gkaa001	journal	February 2020
Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit Stojković, Vanja; Myasnikov, Alexander G.; Young, Iris D. Nucleic Acids Research, Vol. 48, Issue 5 https://doi.org/10.1093/nar/gkaa037	journal	January 2020
Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions Graf, Michael; Arenz, Stefan; Huter, Paul Nucleic Acids Research https://doi.org/10.1093/nar/gkw1272	journal	December 2016
The complete chemical structure of Saccharomyces cerevisiae rRNA: partial pseudouridylation of U2345 in 25S rRNA by snoRNA snR9 Taoka, Masato; Nobe, Yuko; Yamaki, Yuka Nucleic Acids Research, Vol. 44, Issue 18 https://doi.org/10.1093/nar/gkw564	journal	June 2016
Structure of the 70S ribosome from human pathogen Staphylococcus aureus Khusainov, Iskander; Vicens, Quentin; Bochler, Anthony Nucleic Acids Research https://doi.org/10.1093/nar/gkw933	journal	October 2016
Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation Ahmed, Tofayel; Shi, Jian; Bhushan, Shashi Nucleic Acids Research, Vol. 45, Issue 14 https://doi.org/10.1093/nar/gkx499	journal	June 2017
Biogenesis and iron-dependency of ribosomal RNA hydroxylation Kimura, Satoshi; Sakai, Yusuke; Ishiguro, Kensuke Nucleic Acids Research, Vol. 45, Issue 22 https://doi.org/10.1093/nar/gkx969	journal	October 2017
Identification of receptors for UNCG and GNRA Z-turns and their occurrence in rRNA D’Ascenzo, Luigi; Vicens, Quentin; Auffinger, Pascal Nucleic Acids Research, Vol. 46, Issue 15 https://doi.org/10.1093/nar/gky578	journal	July 2018
Landscape of the complete RNA chemical modifications in the human 80S ribosome Taoka, Masato; Nobe, Yuko; Yamaki, Yuka Nucleic Acids Research, Vol. 46, Issue 18 https://doi.org/10.1093/nar/gky811	journal	September 2018
A two-step probing method to compare lysine accessibility across macromolecular complex conformations MacRae, Andrew J.; Coltri, Patricia; Hrabeta-Robinson, Eva RNA Biology https://doi.org/10.1101/448605	journal	October 2018
High-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit and validation of nucleotide modifications Stojković, Vanja; Myasnikov, Alexander G.; Young, Iris D. BioRxiv https://doi.org/10.1101/695429	posted_content	July 2019
Molecular Mimicry of SecA and Signal Recognition Particle Binding to the Bacterial Ribosome Knüpffer, Lara; Fehrenbach, Clara; Denks, Kärt mBio, Vol. 10, Issue 4 https://doi.org/10.1128/mbio.01317-19	journal	August 2019
Nucleobase carbonyl groups are poor Mg ²⁺ inner-sphere binders but excellent monovalent ion binders—a critical PDB survey Leonarski, Filip; D'Ascenzo, Luigi; Auffinger, Pascal RNA, Vol. 25, Issue 2 https://doi.org/10.1261/rna.068437.118	journal	November 2018
Structural evidence for product stabilization by the ribosomal mRNA helicase Amiri, Hossein; Noller, Harry F. RNA, Vol. 25, Issue 3 https://doi.org/10.1261/rna.068965.118	journal	December 2018
Mitochondrial 16S rRNA Is Methylated by tRNA Methyltransferase TRMT61B in All Vertebrates Bar-Yaacov, Dan; Frumkin, Idan; Yashiro, Yuka PLOS Biology, Vol. 14, Issue 9 https://doi.org/10.1371/journal.pbio.1002557	journal	September 2016
The complete structure of the chloroplast 70S ribosome in complex with translation factor pY Bieri, Philipp; Leibundgut, Marc; Saurer, Martin The EMBO Journal, Vol. 36, Issue 4 https://doi.org/10.15252/embj.201695959	journal	December 2016
Visualizing the Role of 2’-OH rRNA Methylations in the Human Ribosome Structure Natchiar, S.; Myasnikov, Alexander; Hazemann, Isabelle Biomolecules, Vol. 8, Issue 4 https://doi.org/10.3390/biom8040125	journal	October 2018
Nervous-Like Circuits in the Ribosome Facts, Hypotheses and Perspectives Timsit, Youri; Bennequin, Daniel International Journal of Molecular Sciences, Vol. 20, Issue 12 https://doi.org/10.3390/ijms20122911	journal	June 2019
Defects in the assembly of ribosomes selected for β-amino acid incorporation Ward, Fred R.; Watson, Zoe L.; Ad, Omer bioRxiv https://doi.org/10.1101/733584	posted_content	August 2019
Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon Ahmad, Jomaa,; Daniel, Boehringer,; Marc, Leibundgut, ETH Zurich https://doi.org/10.3929/ethz-b-000112526	text	January 2016
Structural basis of translation inhibition by cadazolid, a novel quinoxolidinone antibiotic Alain, Scaiola,; Marc, Leibundgut,; Daniel, Boehringer, ETH Zurich https://doi.org/10.3929/ethz-b-000338181	text	January 2019
Mitochondrial 16S rRNA Is Methylated by tRNA Methyltransferase TRMT61B in All Vertebrates Bar-Yaacov, Dan; Frumkin, Idan; Yashiro, Yuka ETH Zurich https://doi.org/10.3929/ethz-b-000121965	text	January 2016
Dissecting ribosomal particles throughout the kingdoms of life using advanced hybrid mass spectrometry methods Van De Waterbeemd, Michiel; Tamara, Sem; Fort, Kyle L. ETH Zurich https://doi.org/10.3929/ethz-b-000274418	text	January 2018
Automated cryo-EM Structure Refinement using Correlation-Driven Molecular Dynamics Vaiana, Andrea C.; Igaev, Maxim; Bock, Lars V. Biophysical Journal, Vol. 118, Issue 3 https://doi.org/10.1016/j.bpj.2019.11.1656	journal	February 2020
Structure of the 70S ribosome from human pathogen Staphylococcus aureus Khusainov, Iskander; Vicens, Quentin; Bochler, Anthony Nucleic Acids Research, Vol. 45, Issue 2 https://doi.org/10.1093/nar/gkw1126	journal	November 2016
Decoding Mammalian Ribosome-mRNA States by Translational GTPase Complexes Shao, Sichen; Murray, Jason; Brown, Alan Cell, Vol. 167, Issue 5 https://doi.org/10.1016/j.cell.2016.10.046	journal	November 2016
Comparative RNA function analysis reveals high functional similarity between distantly related bacterial 16 S rRNAs Tsukuda, Miyuki; Kitahara, Kei; Miyazaki, Kentaro Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-10214-3	journal	August 2017
The fluctuating ribosome: thermal molecular dynamics characterized by neutron scattering Zaccai, Giuseppe; Natali, Francesca; Peters, Judith Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep37138	journal	November 2016
Dynamic contact network between ribosomal subunits enables rapid large-scale rotation during spontaneous translocation Bock, Lars V.; Blau, Christian; Vaiana, Andrea C. Nucleic Acids Research, Vol. 43, Issue 14 https://doi.org/10.1093/nar/gkv649	journal	June 2015
‘Z-DNA like’ fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response D'Ascenzo, Luigi; Leonarski, Filip; Vicens, Quentin Nucleic Acids Research, Vol. 44, Issue 12 https://doi.org/10.1093/nar/gkw388	journal	May 2016
Random pseuoduridylation in vivo reveals critical region of Escherichia coli 23S rRNA for ribosome assembly Leppik, Margus; Liiv, Aivar; Remme, Jaanus Nucleic Acids Research, Vol. 45, Issue 10 https://doi.org/10.1093/nar/gkx160	journal	March 2017
Assaying RNA structure with LASER-Seq Zinshteyn, Boris; Chan, Dalen; England, Whitney Nucleic Acids Research, Vol. 47, Issue 1 https://doi.org/10.1093/nar/gky1172	journal	November 2018
De novo computational RNA modeling into cryoEM maps of large ribonucleoprotein complexes Kappel, Kalli; Liu, Shiheng; Larsen, Kevin P. bioRxiv https://doi.org/10.1101/332791	posted_content	May 2018
Decavanadate Inhibits Mycobacterial Growth More Potently Than Other Oxovanadates Samart, Nuttaporn; Arhouma, Zeyad; Kumar, Santosh Frontiers in Chemistry, Vol. 6 https://doi.org/10.3389/fchem.2018.00519	journal	November 2018
Exploring Wells-Dawson Clusters Associated With the Small Ribosomal Subunit Crans, Debbie C.; Sánchez-Lombardo, Irma; McLauchlan, Craig C. Frontiers in Chemistry, Vol. 7 https://doi.org/10.3389/fchem.2019.00462	journal	July 2019
Ribosomal Antibiotics: Contemporary Challenges Auerbach-Nevo, Tamar; Baram, David; Bashan, Anat Antibiotics, Vol. 5, Issue 3 https://doi.org/10.3390/antibiotics5030024	journal	June 2016

Similar Records

Regulation of Translation by Lysine Acetylation in Escherichia coli

Journal Article · Tue Jun 28 00:00:00 EDT 2022 · mBio (Online) · OSTI ID:1347117

Feid, Sarah C.; Walukiewicz, Hanna E.; Wang, Xiaoyi; +4 more

Sarecycline interferes with tRNA accommodation and tethers mRNA to the 70S ribosome

Journal Article · Wed Aug 12 00:00:00 EDT 2020 · Proceedings of the National Academy of Sciences of the United States of America · OSTI ID:1347117

Batool, Zahra; Lomakin, Ivan B.; Polikanov, Yury S.; +1 more

Cross-linking of streptomycin to the 16S ribosomal RNA of Escherichia coli

Journal Article · Tue Sep 22 00:00:00 EDT 1987 · Biochemistry; (United States) · OSTI ID:1347117

Gravel, M; Melancon, P; Barkier-Gingras, L

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
drug recovery
evolution
single-molecule biophysics
X-ray crystallography

Title: High-resolution structure of the Escherichia coli ribosome

Citation Formats

References (82)

Cited By (60)

Similar Records

Related Subjects