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Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-TuH84A.

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Fislage M, Zhang J, Brown ZP, Mandava CS, Sanyal S, Ehrenberg M, Frank J
OpenAccess logo Nucleic Acids Res 46 5861-5874 (2018)
Related entries: 5wdt, 5we4, 5wf0, 5wfk, 5wfs

Cited: 20 times
EuropePMC logo PMID: 29733411

Abstract

The GTPase EF-Tu in ternary complex with GTP and aminoacyl-tRNA (aa-tRNA) promotes rapid and accurate delivery of cognate aa-tRNAs to the ribosomal A site. Here we used cryo-EM to study the molecular origins of the accuracy of ribosome-aided recognition of a cognate ternary complex and the accuracy-amplifying role of the monitoring bases A1492, A1493 and G530 of the 16S rRNA. We used the GTPase-deficient EF-Tu variant H84A with native GTP, rather than non-cleavable GTP analogues, to trap a near-cognate ternary complex in high-resolution ribosomal complexes of varying codon-recognition accuracy. We found that ribosome complexes trapped by GTPase-deficicent ternary complex due to the presence of EF-TuH84A or non-cleavable GTP analogues have very similar structures. We further discuss speed and accuracy of initial aa-tRNA selection in terms of conformational changes of aa-tRNA and stepwise activation of the monitoring bases at the decoding center of the ribosome.

Articles - 5we6 mentioned but not cited (1)

  1. Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-TuH84A. Fislage M, Zhang J, Brown ZP, Mandava CS, Sanyal S, Ehrenberg M, Frank J. Nucleic Acids Res 46 5861-5874 (2018)


Reviews citing this publication (3)

  1. The Structural Dynamics of Translation. Korostelev AA. Annu Rev Biochem 91 245-267 (2022)
  2. Advances in domain and subunit localization technology for electron microscopy. Brown ZP, Takagi J. Biophys Rev 11 149-155 (2019)
  3. Diversity and Similarity of Termination and Ribosome Rescue in Bacterial, Mitochondrial, and Cytoplasmic Translation. Korostelev AA. Biochemistry (Mosc) 86 1107-1121 (2021)

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  2. Cryo-EM of elongating ribosome with EF-Tu•GTP elucidates tRNA proofreading. Loveland AB, Demo G, Korostelev AA. Nature 584 640-645 (2020)
  3. Elongation factor-Tu can repetitively engage aminoacyl-tRNA within the ribosome during the proofreading stage of tRNA selection. Morse JC, Girodat D, Burnett BJ, Holm M, Altman RB, Sanbonmatsu KY, Wieden HJ, Blanchard SC. Proc Natl Acad Sci U S A 117 3610-3620 (2020)
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  5. findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM. Chojnowski G, Simpkin AJ, Leonardo DA, Seifert-Davila W, Vivas-Ruiz DE, Keegan RM, Rigden DJ. IUCrJ 9 86-97 (2022)
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  7. Structural and molecular basis for Cardiovirus 2A protein as a viral gene expression switch. Hill CH, Pekarek L, Napthine S, Kibe A, Firth AE, Graham SC, Caliskan N, Brierley I. Nat Commun 12 7166 (2021)
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  11. Kinetic Analysis Suggests Evolution of Ribosome Specificity in Modern Elongation Factor-Tus from "Generalist" Ancestors. De Tarafder A, Parajuli NP, Majumdar S, Kaçar B, Sanyal S. Mol Biol Evol 38 3436-3444 (2021)
  12. Network theory of the bacterial ribosome. Calvet LE, Matviienko S, Ducluzaux P. PLoS One 15 e0239700 (2020)
  13. Genetic code degeneracy is established by the decoding center of the ribosome. Ye S, Lehmann J. Nucleic Acids Res 50 4113-4126 (2022)
  14. Geometric alignment of aminoacyl-tRNA relative to catalytic centers of the ribosome underpins accurate mRNA decoding. Girodat D, Wieden HJ, Blanchard SC, Sanbonmatsu KY. Nat Commun 14 5582 (2023)
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  16. Transient disome complex formation in native polysomes during ongoing protein synthesis captured by cryo-EM. Flügel T, Schacherl M, Unbehaun A, Schroeer B, Dabrowski M, Bürger J, Mielke T, Sprink T, Diebolder CA, Guillén Schlippe YV, Spahn CMT. Nat Commun 15 1756 (2024)


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