Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

A ratchet-like inter-subunit reorganization of the ribosome during translocation

Nature volume 406, pages 318–322 (2000)Cite this article

Abstract

The ribosome is a macromolecular assembly that is responsible for protein biosynthesis following genetic instructions in all organisms. It is composed of two unequal subunits: the smaller subunit binds messenger RNA and the anticodon end of transfer RNAs, and helps to decode the mRNA; and the larger subunit interacts with the amino-acid-carrying end of tRNAs and catalyses the formation of the peptide bonds. After peptide-bond formation, elongation factor G (EF-G) binds to the ribosome, triggering the translocation of peptidyl-tRNA from its aminoacyl site to the peptidyl site, and movement of mRNA by one codon1. Here we analyse three-dimensional cryo-electron microscopy maps of the Escherichia coli 70S ribosome in various functional states, and show that both EF-G binding and subsequent GTP hydrolysis lead to ratchet-like rotations of the small 30S subunit relative to the large 50S subunit. Furthermore, our finding indicates a two-step mechanism of translocation: first, relative rotation of the subunits and opening of the mRNA channel following binding of GTP to EF-G; and second, advance of the mRNA/(tRNA)2 complex in the direction of the rotation of the 30S subunit, following GTP hydrolysis.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Stereo representation of the rotational movement of the 30S subunit (yellow) with respect to 50S subunit (blue) upon EF-G (red) binding.
Figure 2: Effect of EF-G-dependent GTP hydrolysis on the dynamics of the mRNA channel.
Figure 3: Effect of rotation on the tRNA position before and after GTP hydrolysis.
Figure 4: Diagram showing three steps of the translocation process.

Similar content being viewed by others

References

  1. Wilson, K. S. & Noller, H. F. Molecular movement inside the translational engine. Cell 92, 337– 349 (1998).

    Article  CAS  Google Scholar 

  2. Malhotra, A. et al. Escherichia coli 70 S ribosome at 15 Å resolution by cryo-electron microscopy: localization of fMet-tRNAMet f and fitting of L1 protein. J. Mol. Biol. 280 , 103–116 (1998).

    Article  CAS  Google Scholar 

  3. Agrawal, R. K., Heagle, A. B., Penczek, P., Grassucci, R. A. & Frank, J. EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome. Nature Struct. Biol. 6, 643– 647 (1999).

    Article  CAS  Google Scholar 

  4. Agrawal, R. K., Penczek, P., Grassucci, R. A. & Frank, J. Visualization of elongation factor G on the Escherichia coli 70S ribosome: the mechanism of translocation. Proc. Natl Acad. Sci. USA. 95, 6134–6138 (1998).

    Article  ADS  CAS  Google Scholar 

  5. Agrawal, R. K., Heagle, A. B. & Frank, J. in The Ribosome: Structure, Function, Antibiotics, and Cellular Interactions (eds Garrett, R. A. et al.) 53– 62 (ASM, Washington DC, 2000).

    Book  Google Scholar 

  6. Spirin, A. S., Baranov, V. I., Polubesov, G. S., Serdyuk, I. N. & May, R. P. Translocation makes the ribosome less compact. J. Mol. Biol. 194, 119– 128 (1987).

    Article  CAS  Google Scholar 

  7. Serdyuk, I. et al. Structural dynamics of translating ribosomes. Biochimie 74, 299–306 ( 1992).

    Article  CAS  Google Scholar 

  8. Frank, J. et al. A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome. Nature 376, 441–444 (1995).

    Article  ADS  CAS  Google Scholar 

  9. Agrawal, R. K. et al. Direct visualization of A-, P-, and E-site transfer RNAs in the Escherichia coli ribosome. Science 271, 1000–1002 (1996).

    Article  ADS  CAS  Google Scholar 

  10. Mueller, F., Stark, H., van Heel, M., Rinke-Appel, J. & Brimacombe, R. A new model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA. III. The topography of the functional centre. J. Mol. Biol. 271, 566– 587 (1997).

    Article  CAS  Google Scholar 

  11. Frank, J. et al. in The Ribosome: Structure, Function, Antibiotics, and Cellular Interactions (eds Garrett, R. A. et al.) 45-51 (ASM, Washington DC, 2000).

    Google Scholar 

  12. Lata, K. R. et al. Three-dimensional reconstruction of the Escherichia coli 30 S ribosomal subunit in ice. J. Mol. Biol. 262 , 43–52 (1996).

    Article  CAS  Google Scholar 

  13. Agrawal, R. K., Lata, R. K. & Frank, J. Conformational variability in Escherichia coli 70S ribosome as revealed by 3D cryo-electron microscopy. Int. J. Biochem. Cell Biol. 31, 243–254 (1999).

    Article  CAS  Google Scholar 

  14. Powers, T. & Noller, H. F. The 530 loop of 16S rRNA: a signal to EF-Tu? Trends Genet. 10, 27– 31 (1994).

    Article  CAS  Google Scholar 

  15. Newcomb, L. F. & Noller, H. F. Directed hydroxyl radical probing of 16S rRNA in the ribosome: spatial proximity of RNA elements of the 3′ and 5′ domains. RNA 5, 849–855 (1999).

    Article  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  17. Agrawal, R. K. et al. Visualization of tRNA movements on the E. coli ribosome during the elongation cycle. J. Cell. Biol. (in the press).

  18. Gabashvili, I. S. et al. Solution structure of the E. coli 70S ribosome at 11. 5 Å resolution. Cell 100, 537– 549 (2000).

    Article  CAS  Google Scholar 

  19. Cate, J. H., Yusupov, M. M., Yusupova, G. Z., Earnest, T. N. & Noller, H. F. X-ray crystal structures of 70S ribosome functional complexes. Science 285, 2095–2104 (1999).

    Article  CAS  Google Scholar 

  20. Clemons, W. M. et al. Structure of a bacterial 30S ribosomal subunit at 5.5 Å resolution. Nature 400, 833– 840 (1999).

    Article  ADS  CAS  Google Scholar 

  21. Stark, H. et al. Arrangement of tRNAs in pre- and posttranslocational ribosomes revealed by electron cryomicroscopy. Cell 88, 19–28 (1997).

    Article  CAS  Google Scholar 

  22. Nissen, P. et al. Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. Science 270, 1464–1472 (1995).

    Article  ADS  CAS  Google Scholar 

  23. Stark, H. et al. Visualization of elongation factor Tu on the Escherichia coli ribosome. Nature 389, 403– 406 (1997).

    Article  ADS  CAS  Google Scholar 

  24. Stark, H., Rodnina, M. V., Wieden, H. -J., van Heel, M. & Wintermeyer, W. Large scale movement of elongation factor G and extensive conformational change of the ribosome during translocation. Cell 100, 301–309 (2000).

    Article  CAS  Google Scholar 

  25. Porse, B. T., Leviev, I., Mankin, A. S. & Garrett, R. A. The antibiotic thiostrepton inhibits a functional transition within protein L11 at the ribosomal GTPase center. J. Mol. Biol. 276 , 391–404 (1998).

    Article  CAS  Google Scholar 

  26. Bretscher, M. S. Translocation in protein synthesis: A hybrid structure model. Nature 218, 675–677 ( 1968).

    Article  ADS  CAS  Google Scholar 

  27. Spirin, A. S. A model of the functioning ribosome: locking and unlocking of the ribosome subparticles. Cold Spring Harbor Symp. Quant. Biol. 34, 197–207 (1969).

    Article  CAS  Google Scholar 

  28. Woese, C. Molecular mechanics of translation: a reciprocating ratchet mechanism. Nature 226, 817–820 ( 1970).

    Article  ADS  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  30. Agrawal, R. K. & Burma, D. P. Sites of ribosomal RNAs involved in the subunit association of tight and loose couple ribosomes. J. Biol. Chem. 271, 21285– 21291 (1996).

    Article  CAS  Google Scholar 

  31. Frank, J. et al. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 116, 190–199 (1996).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by grants from the National Institutes of Health. We thank A. Heagle for preparing the illustrations and animated sequence, and I. Gabashvili and P. Penczek for help with image processing.

Author information

Authors and Affiliations

  1. Howard Hughes Medical Institute, ,

    Joachim Frank

  2. Health Research Incorporated at the Wadsworth Center,

    Joachim Frank & Rajendra Kumar Agrawal

  3. Department of Biomedical Sciences, State University of New York at Albany, Empire State Plaza, PO Box 509, Albany, 12201-0509, New York, USA

    Joachim Frank & Rajendra Kumar Agrawal

Authors
  1. Joachim Frank
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Rajendra Kumar Agrawal
    View author publications

    You can also search for this author in PubMed Google Scholar

Supplementary information

41586_2000_BF35018597_MOESM1_ESM.mov

Movie: The Ribosome — a molecular ratchet. For instructions on how to play this movie, please visit http://www.quicktime.com (MOV 2534 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Frank, J., Agrawal, R. A ratchet-like inter-subunit reorganization of the ribosome during translocation . Nature 406, 318–322 (2000). https://doi.org/10.1038/35018597

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/35018597

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing