Structural aspects of messenger RNA reading frame maintenance by the ribosome

<i>Coot</i> : model-building tools for molecular graphics

Emsley, P., & Cowtan, K. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904019158 · Cited by 30,571 · see citing works

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse‐Kunstleve, R. W., Jiang, J., Kuszewski, J. J., Nilges, M., Pannu, N., et al. (1998) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444998003254 · Cited by 15,720 · see citing works

The 3′-Terminal Sequence of Escherichia coli 16S Ribosomal RNA: Complementarity to Nonsense Triplets and Ribosome Binding Sites

Shine, J., & Dalgarno, L. (1974) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.71.4.1342 · Cited by 3,628 · see citing works

Purification and Characterization

Tsai, C. S. (2006) · Biomacromolecules · doi:10.1002/0470080124.ch3 · Cited by 2,368 · see citing works

Crystal structure of the ribosome at 5.5 Å resolution

Yusupov, M. M., Yusupova, G. Z., Baucom, A., Lieberman, K., Earnest, T. N., Cate, J. H. D., & Noller, H. F. (2001) · Science · doi:10.1126/science.1060089 · Cited by 1,944 · see citing works

Evaluation of single-crystal X-ray diffraction data from a position-sensitive detector

Kabsch, W. (1988) · Journal of Applied Crystallography · doi:10.1107/s0021889888007903 · Cited by 1,509 · see citing works

Structure of the 70S Ribosome Complexed with mRNA and tRNA

Selmer, M., Dunham, C., Murphy, F., Weixlbaumer, A., Petry, S., Kelley, A. C., Weir, J., & Ramakrishnan, V. (2006) · Science · doi:10.1126/science.1131127 · Cited by 1,352 · see citing works

Version 1.2 of the Crystallography and NMR system

Brünger, A. T. (2007) · Nature Protocols · doi:10.1038/nprot.2007.406 · Cited by 1,325 · see citing works

Recognition of Cognate Transfer RNA by the 30 <i>S</i> Ribosomal Subunit

Ogle, J. M., Brodersen, D. E., Clemons, W. M., Tarry, M. J., Carter, A. P., & Ramakrishnan, V. (2001) · Science · doi:10.1126/science.1060612 · Cited by 1,162 · see citing works

Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form

Ogle, J. M., Murphy, F. V., Tarry, M. J., & Ramakrishnan, V. (2002) · Cell · doi:10.1016/s0092-8674(02)01086-3 · Cited by 663 · see citing works

The Path of Messenger RNA through the Ribosome

Yusupova, G. Z., Yusupov, M., Cate, J. H. D., & Noller, H. F. (2001) · Cell · doi:10.1016/s0092-8674(01)00435-4 · Cited by 597 · see citing works

Locking and Unlocking of Ribosomal Motions

Valle, M., Zavialov, A. V., Sengupta, J., Rawat, U. B. S., Ehrenberg, M., & Frank, J. (2003) · Cell · doi:10.1016/s0092-8674(03)00476-8 · Cited by 590 · see citing works

Automatic indexing of rotation diffraction patterns

Kabsch, W. (1988) · Journal of Applied Crystallography · doi:10.1107/s0021889887009737 · Cited by 566 · see citing works

Improvement of reading frame maintenance is a common function for several tRNA modifications

Urbonavičius, J., Qian, Q., Durand, J. M. B., Hagervall, T. G., & Björk, G. R. (2001) · The EMBO Journal · doi:10.1093/emboj/20.17.4863 · Cited by 499 · see citing works

Crystal Structure of a 70S Ribosome-tRNA Complex Reveals Functional Interactions and Rearrangements

Korostelev, A., Trakhanov, S., Laurberg, M., & Noller, H. F. (2006) · Cell · doi:10.1016/j.cell.2006.08.032 · Cited by 498 · see citing works

The RNA Modification Database: 1999 update

Rozenski, J., Crain, P. F., & McCloskey, J. A. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.196 · Cited by 390 · see citing works

Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation

Spahn, C. M. T., Gómez-Lorenzo, M. G., Grassucci, R. A., Jørgensen, R., Andersen, G. R., Beckmann, R., Penczek, P. A., Ballesta, J. P. G., & Frank, J. (2004) · The EMBO Journal · doi:10.1038/sj.emboj.7600102 · Cited by 385 · see citing works

Metal ions in the structure and function of RNA

Pyle, A. M. (2002) · JBIC Journal of Biological Inorganic Chemistry · doi:10.1007/s00775-002-0387-6 · Cited by 378 · see citing works

The role of modifications in codon discrimination by tRNALysUUU

Murphy, F. V., Ramakrishnan, V., Małkiewicz, A. J., & Agris, P. F. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb861 · Cited by 360 · see citing works

Structural basis for translation termination on the 70S ribosome

Laurberg, M., Asahara, H., Korostelev, A. A., Zhu, J., Trakhanov, S. D., & Noller, H. F. (2008) · Nature · doi:10.1038/nature07115 · Cited by 357 · see citing works

The contribution of metal ions to the structural stability of the large ribosomal subunit

Klein, D. J., Moore, P. B., & Steitz, T. A. (2004) · RNA · doi:10.1261/rna.7390804 · Cited by 330 · see citing works

Insights into Translational Termination from the Structure of RF2 Bound to the Ribosome

Weixlbaumer, A., Jin, H. R., Neubauer, C., et al. (2008) · Science · doi:10.1126/science.1164840 · Cited by 308 · see citing works

Structural basis for messenger RNA movement on the ribosome

Yusupova, G. Z., Jenner, L. B., Rees, B., Moras, D., & Yusupov, M. (2006) · Nature · doi:10.1038/nature05281 · Cited by 264 · see citing works

Structures of the Ribosome in Intermediate States of Ratcheting

Zhang, W., Dunkle, J. A., & Cate, J. H. D. (2009) · Science · doi:10.1126/science.1175275 · Cited by 258 · see citing works

Crystal structure of a translation termination complex formed with release factor RF2

Korostelev, A. A., Asahara, H., Lancaster, L., Laurberg, M., Hirschi, A., Zhu, J., Trakhanov, S. D., Scott, W. G., & Noller, H. F. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0810953105 · Cited by 254 · see citing works

tRNA's modifications bring order to gene expression

Gustilo, E. M., Vendeix, F. A. P., & Agris, P. F. (2008) · Current Opinion in Microbiology · doi:10.1016/j.mib.2008.02.003 · Cited by 240 · see citing works

Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines

Weixlbaumer, A., Murphy, F. V., Dziergowska, A., Małkiewicz, A. J., Vendeix, F. A. P., Agris, P. F., & Ramakrishnan, V. (2007) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1242 · Cited by 196 · see citing works

Processivity errors of gene expression in Escherichia coli

Jørgensen, F., & Kurland, C. G. (1990) · Journal of Molecular Biology · doi:10.1016/s0022-2836(05)80164-0 · Cited by 140 · see citing works

Possibilities for the Evolution of the Genetic Code from a Preceding Form

Jukes, T. H. (1973) · Nature · doi:10.1038/246022a0 · Cited by 131 · see citing works

Mutations affecting tRNATrp and its charging and their effect on regulation of transcription termination at the attenuator of the tryptophan operon

Yanofsky, C., & Soll, L. (1977) · Journal of Molecular Biology · doi:10.1016/0022-2836(77)90229-7 · Cited by 129 · see citing works

Crystal structure of the ribosome recycling factor bound to the ribosome

Weixlbaumer, A., Petry, S., Dunham, C. M., et al. (2007) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1282 · Cited by 105 · see citing works

Transfer RNA modifications that alter +1 frameshifting in general fail to affect −1 frameshifting

Urbonavičius, J., Stahl, G., Durand, J. M. B., et al. (2003) · RNA · doi:10.1261/rna.5210803 · Cited by 104 · see citing works

Translational Operator of mRNA on the Ribosome: How Repressor Proteins Exclude Ribosome Binding

Jenner, L. B., Romby, P., Rees, B., et al. (2005) · Science · doi:10.1126/science.1105639 · Cited by 101 · see citing works

Influence of modification next to the anticodon in tRNA on codon context sensitivity of translational suppression and accuracy

Bouadloun, F., Srichaiyo, T., Isaksson, L. A., & Björk, G. R. (1986) · Journal of Bacteriology · doi:10.1128/jb.166.3.1022-1027.1986 · Cited by 94 · see citing works

The role of 2-methylthio-N6-isopentenyladenosine in readthrough and suppression of nonsense codons in Escherichia coli

Petrullo, L. A., Gallagher, P. J., & Elseviers, D. (1983) · Molecular and General Genetics MGG · doi:10.1007/bf00330653 · Cited by 94 · see citing works

Identification and characterization ofE.coliribosomal binding sites by free energy computation

Schurr, T., Nadir, E., & Margalit, H. (1993) · Nucleic Acids Research · doi:10.1093/nar/21.17.4019 · Cited by 88 · see citing works

The effect of point mutations affecting Escherichia coli tryptophan tRNA on anticodon-anticodon interactions and on UGA suppression

Vacher, J., Grosjean, H., Houssier, C., et al. (1984) · Journal of Molecular Biology · doi:10.1016/0022-2836(84)90460-1 · Cited by 72 · see citing works

Presence of the hypermodified nucleotide N6-(delta 2-isopentenyl)-2-methylthioadenosine prevents codon misreading by Escherichia coli phenylalanyl-transfer RNA.

Wilson, R. K., & Roe, B. A. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.2.409 · Cited by 71 · see citing works

Destabilization of codon-anticodon interaction in the ribosomal exit site

Lill, R., & Wintermeyer, W. (1987) · Journal of Molecular Biology · doi:10.1016/0022-2836(87)90516-x · Cited by 70 · see citing works

Significance of the third tRNA binding site, the E site, on E. coli ribosomes for the accuracy of translation: an occupied E site prevents the binding of non‐cognate aminoacyl‐tRNA to the A site.

Geigenmüller, U., & Nierhaus, K. H. (1990) · The EMBO Journal · doi:10.1002/j.1460-2075.1990.tb07904.x · Cited by 68 · see citing works

Messenger RNA conformations in the ribosomal E site revealed by X‐ray crystallography

Jenner, L. B., Rees, B., Yusupov, M., & Yusupova, G. Z. (2007) · EMBO Reports · doi:10.1038/sj.embor.7401044 · Cited by 59 · see citing works

Function of Modified Nucleosides 7-Methylguanosine, Ribothymidine, and 2-Thiomethyl- N 6 -(Isopentenyl)adenosine in Procaryotic Transfer Ribonucleic Acid

Hoburg, A., Aschhoff, H. J., Kersten, H., et al. (1979) · Journal of Bacteriology · doi:10.1128/jb.140.2.408-414.1979 · Cited by 21 · see citing works

Study of tyrosine transfer ribonucleic acid modification in relation to sporulation in Bacillus subtilis

Menichi, B., & Heyman, T. (1976) · Journal of Bacteriology · doi:10.1128/jb.127.1.268-280.1976 · Cited by 21 · see citing works

Effect of modification of tRNA nucleotide 37 on the tRNA interaction with the A and P sites of the Escherichia coli 70S ribosome

Konevega, A. L., Soboleva, N. G., Makhno, V. I., et al. (2006) · Molecular Biology · doi:10.1134/s0026893306040121 · Cited by 16 · see citing works

[The effect of modification of tRNA nucleotide-37 on the tRNA interaction with the P- and A-site of the 70S ribosome Escherichia coli].

Konevega, A. L., Ng, S., Makhno, V. I., et al. (2006) · PubMed · Cited by 11 · see citing works

One core, two shells: bacterial and eukaryotic ribosomes

Melnikov, S., Ben-Shem, A., Garreau de Loubresse, N., Jenner, L., Yusupova, G., & Yusupov, M. (2012) · Nature Structural &amp; Molecular Biology · doi:10.1038/nsmb.2313 · Cited by 477 · see citing works

An integrated, structure- and energy-based view of the genetic code

Grosjean, H., & Westhof, E. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw608 · Cited by 278 · see citing works

Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation

Zhou, J., Lancaster, L., Donohue, J. P., & Noller, H. F. (2013) · Science · doi:10.1126/science.1236086 · Cited by 229 · see citing works

Structural basis for potent inhibitory activity of the antibiotic tigecycline during protein synthesis

Jenner, L., Starosta, A. L., Terry, D. S., Mikolajka, A., Filonava, L., Yusupov, M., Blanchard, S. C., Wilson, D. N., & Yusupova, G. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1216691110 · Cited by 204 · see citing works

Structure of the SecY channel during initiation of protein translocation

Park, E., Ménétret, J.-F., Gumbart, J. C., Ludtke, S. J., Li, W., Whynot, A., Rapoport, T. A., & Akey, C. W. (2014) · Nature · doi:10.1038/nature12720 · Cited by 148 · see citing works

SecM-Stalled Ribosomes Adopt an Altered Geometry at the Peptidyl Transferase Center

Bhushan, S., Hoffmann, T., Seidelt, B., Frauenfeld, J., Mielke, T., Berninghausen, O., Wilson, D. N., & Beckmann, R. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1000581 · Cited by 154 · see citing works

Impact of methylations of m2G966/m5C967 in 16S rRNA on bacterial fitness and translation initiation

Burakovsky, D. E., Prokhorova, I. V., Sergiev, P. V., Milón, P., Sergeeva, O. V., Bogdanov, A. A., Rodnina, M. V., & Dontsova, O. A. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks508 · Cited by 61 · see citing works

Resistance mutations generate divergent antibiotic susceptibility profiles against translation inhibitors

Cocozaki, A. I., Altman, R. B., Huang, J., Buurman, E. T., Kazmirski, S. L., Doig, P., Prince, D. B., Blanchard, S. C., Cate, J. H. D., & Ferguson, A. D. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1605127113 · Cited by 56 · see citing works

Metals in Motion: Understanding Labile Metal Pools in Bacteria

Helmann, J. D. (2025) · Biochemistry · doi:10.1021/acs.biochem.4c00726 · Cited by 49 · see citing works

On the Role of the P-site in Leftward Ribosome Frameshifting at a Hungry Codon

Kolor, K., Lindsley, D., & Gallant, J. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1118 · Cited by 20 · see citing works

Dynamic pathways of −1 translational frameshifting

Chen, J., Petrov, A. N., Johansson, M., Tsai, A., O’Leary, S. E., & Puglisi, J. D. (2014) · Nature · doi:10.1038/nature13428 · Cited by 159 · see citing works

Ribosomal tRNA Binding Sites: Three-Site Models of Translation

Burkhardt, N., Jünemann, R., Spahn, C. M. T., & Nierhaus, K. H. (1998) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409239891204189 · Cited by 51 · see citing works

Recognition and Positioning of mRNA in the Ribosome by tRNAs with Expanded Anticodons

Walker, S. E., & Fredrick, K. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.05.006 · Cited by 43 · see citing works

Extending the Spacing between the Shine–Dalgarno Sequence and P-Site Codon Reduces the Rate of mRNA Translocation

Wakabayashi, H., Warnasooriya, C., & Ermolenko, D. N. (2020) · Journal of Molecular Biology · doi:10.1016/j.jmb.2020.06.008 · Cited by 9 · see citing works