Skip to main content

Thank you for visiting 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.

Functional epitopes at the ribosome subunit interface


The ribosome is a 2.5-MDa molecular machine that synthesizes cellular proteins encoded in mRNAs1. The 30S and 50S subunits of the ribosome associate through structurally defined intersubunit bridges2,3,4,5 burying 6,000 Å2, 80% of which is buried in conserved RNA-RNA interactions6. Intersubunit bridges bind translation factors7,8, may coordinate peptide bond formation and translocation9,10,11 and may be actively remodeled in the post-termination complex12,13, but the functional importance of numerous 30S bridge nucleotides had been unknown. We carried out large-scale combinatorial mutagenesis and in vivo selections on 30S nucleotides that form RNA-RNA intersubunit bridges in the Escherichia coli ribosome. We determined the covariation and functional importance of bridge nucleotides, allowing comparison of the structural interface and phylogenetic data to the functional epitope. Our results reveal how information for ribosome function is partitioned across bridges, and suggest a subset of nucleotides that may have measurable effects on individual steps of the translational cycle.

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

Access options

Rent or buy this article

Prices vary by article type



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

Figure 1: Selection of functional ribosome intersubunit bridges.
Figure 2: Intersubunit bridges.
Figure 3: Covariation between 16S rRNA intersubunit bridge nucleotide positions.
Figure 4: Functional epitopes in structurally defined intersubunit bridges and interactions between 30S intersubunit bridge nucleotides and 50S.
Figure 5: Function and phylogenetic conservation in intersubunit bridge nucleotides.

Accession codes


Protein Data Bank


  1. Ramakrishnan, V. Ribosome structure and the mechanism of translation. Cell 108, 557–572 (2002).

    Article  CAS  Google Scholar 

  2. Frank, J. et al. A model of the translational apparatus based on a three-dimensional reconstruction of the Escherichia coli ribosome. Biochem. Cell Biol. 73, 757–765 (1995).

    Article  CAS  Google Scholar 

  3. Gabashvili, I.S. et al. Solution structure of the E. coli 70S ribosome at 11.5 A resolution. Cell 100, 537–549 (2000).

    Article  CAS  Google Scholar 

  4. Yusupov, M.M. et al. Crystal structure of the ribosome at 5.5 A resolution. Science 292, 883–896 (2001).

    Article  CAS  Google Scholar 

  5. Schuwirth, B.S. et al. Structures of the bacterial ribosome at 3.5 A resolution. Science 310, 827–834 (2005).

    Article  CAS  Google Scholar 

  6. Mears, J.A. et al. Modeling a minimal ribosome based on comparative sequence analysis. J. Mol. Biol. 321, 215–234 (2002).

    Article  CAS  Google Scholar 

  7. Tapprich, W.E., Goss, D.J. & Dahlberg, A.E. Mutation at position 791 in Escherichia coli 16S ribosomal RNA affects processes involved in the initiation of protein synthesis. Proc. Natl. Acad. Sci. USA 86, 4927–4931 (1989).

    Article  CAS  Google Scholar 

  8. Cunningham, P.R., Nurse, K., Weitzmann, C.J. & Ofengand, J. Functional effects of base changes which further define the decoding center of Escherichia coli 16S ribosomal RNA: mutation of C1404, G1405, C1496, G1497, and U1498. Biochemistry 32, 7172–7180 (1993).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  10. Gao, H. et al. Study of the structural dynamics of the E. coli 70S ribosome using real-space refinement. Cell 113, 789–801 (2003).

    Article  CAS  Google Scholar 

  11. Valle, M. et al. Locking and unlocking of ribosomal motions. Cell 114, 123–134 (2003).

    Article  CAS  Google Scholar 

  12. Gao, N. et al. Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies. Mol. Cell 18, 663–674 (2005).

    Article  CAS  Google Scholar 

  13. Hirokawa, G. et al. The role of ribosome recycling factor in dissociation of 70S ribosomes into subunits. RNA 11, 1317–1328 (2005).

    Article  CAS  Google Scholar 

  14. Rackham, O. & Chin, J.W. A network of orthogonal ribosome•mRNA pairs. Nat. Chem. Biol. 1, 159–166 (2005).

    Article  CAS  Google Scholar 

  15. Hui, A.S., Eaton, D.H. & de Boer, H.A. Mutagenesis at the mRNA decoding site in the 16S ribosomal RNA using the specialized ribosome system in Escherichia coli. EMBO J. 7, 4383–4388 (1988).

    Article  CAS  Google Scholar 

  16. Hui, A. & de Boer, H.A. Specialized ribosome system: preferential translation of a single mRNA species by a subpopulation of mutated ribosomes in Escherichia coli. Proc. Natl. Acad. Sci. USA 84, 4762–4766 (1987).

    Article  CAS  Google Scholar 

  17. Lee, K., Varma, S., SantaLucia, J., Jr. & Cunningham, P.R. In vivo determination of RNA structure-function relationships: analysis of the 790 loop in ribosomal RNA. J. Mol. Biol. 269, 732–743 (1997).

    Article  CAS  Google Scholar 

  18. Morosyuk, S.V., SantaLucia, J., Jr. & Cunningham, P.R. Structure and function of the conserved 690 hairpin in Escherichia coli 16 S ribosomal RNA. III. Functional analysis of the 690 loop. J. Mol. Biol. 307, 213–228 (2001).

    Article  CAS  Google Scholar 

  19. Triman, K.L., Peister, A. & Goel, R.A. Expanded versions of the 16S and 23S ribosomal RNA mutation databases (16SMDBexp and 23SMDBexp). Nucleic Acids Res. 26, 280–284 (1998).

    Article  CAS  Google Scholar 

  20. Santer, M. et al. Base changes at position 792 of Escherichia coli 16S rRNA affect assembly of 70S ribosomes. Proc. Natl. Acad. Sci. USA 87, 3700–3704 (1990).

    Article  CAS  Google Scholar 

  21. Ghosh, S. & Joseph, S. Nonbridging phosphate oxygens in 16S rRNA important for 30S subunit assembly and association with the 50S ribosomal subunit. RNA 11, 657–667 (2005).

    Article  CAS  Google Scholar 

  22. Belanger, F., Gagnon, M.G., Steinberg, S.V., Cunningham, P.R. & Brakier-Gingras, L. Study of the functional interaction of the 900 tetraloop of 16S ribosomal RNA with helix 24 within the bacterial ribosome. J. Mol. Biol. 338, 683–693 (2004).

    Article  CAS  Google Scholar 

  23. Nissen, P., Ippolito, J.A., Ban, N., Moore, P.B. & Steitz, T.A. RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc. Natl. Acad. Sci. USA 98, 4899–4903 (2001).

    Article  CAS  Google Scholar 

  24. Doherty, E.A., Batey, R.T., Masquida, B. & Doudna, J.A. A universal mode of helix packing in RNA. Nat. Struct. Biol. 8, 339–343 (2001).

    Article  CAS  Google Scholar 

  25. Meier, N. et al. The importance of individual nucleotides for the structure and function of rRNA molecules in E. coli. A mutagenesis study. FEBS Lett. 204, 89–95 (1986).

    Article  CAS  Google Scholar 

  26. Rottmann, N., Kleuvers, B., Atmadja, J. & Wagner, R. Mutants with base changes at the 3′-end of the 16S RNA from Escherichia coli. Construction, expression and functional analysis. Eur. J. Biochem. 177, 81–90 (1988).

    Article  CAS  Google Scholar 

  27. Wimberly, B.T. et al. Structure of the 30S ribosomal subunit. Nature 407, 327–339 (2000).

    Article  CAS  Google Scholar 

  28. Cannone, J.J. et al. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3, 2 (2002).

    Article  Google Scholar 

  29. Moore, P.B. The ribosome in the 21st century: the post-structural era. Cold Spring Harb. Symp. Quant. Biol. 66, 607–614 (2001).

    Article  CAS  Google Scholar 

  30. Jamieson, A.C., Kim, S.H. & Wells, J.A. In vitro selection of zinc fingers with altered DNA-binding specificity. Biochemistry 33, 5689–5695 (1994).

    Article  CAS  Google Scholar 

Download references


J.W.C. is an EMBO Young Investigator. K.W. is grateful for a Medical Research Council–Laboratory of Molecular Biology (MRC-LMB) Cambridge Scholarship, an Honorary External Research Studentship from Trinity College, Cambridge and an Overseas Research Studentship Award. We thank M.E. Hurles (Sanger Institute) for discussions on quantifying sequence polymorphisms, P.H. Dear (LMB) and G. Mitchison (Cambridge) for discussions on statistical methods, and T.M. Schmeing (LMB) and other members of LMB for critically reading versions of the manuscript.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Jason W Chin.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Table 1

Library design. (PDF 10 kb)

Supplementary Table 2

Mutagenic oligonucleotides for multiposition libraries. (PDF 11 kb)

Supplementary Table 3

Library constructed statistics. (PDF 12 kb)

Supplementary Table 4

Selected sequences. (PDF 35 kb)

Supplementary Table 5

Covariation analysis. (PDF 16 kb)

Supplementary Table 6

Intersubunit bridge selection data and phylogenetic data. (PDF 18 kb)

Supplementary Methods (PDF 49 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Rackham, O., Wang, K. & Chin, J. Functional epitopes at the ribosome subunit interface. Nat Chem Biol 2, 254–258 (2006).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


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