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:

Structure of the E. coli signal recognition particle bound to a translating ribosome

Nature volume 444, pages 503–506 (2006)Cite this article

A Corrigendum to this article was published on 30 August 2007

Abstract

The prokaryotic signal recognition particle (SRP) targets membrane proteins into the inner membrane1,2,3,4. It binds translating ribosomes and screens the emerging nascent chain for a hydrophobic signal sequence, such as the transmembrane helix of inner membrane proteins. If such a sequence emerges, the SRP binds tightly, allowing the SRP receptor to lock on. This assembly delivers the ribosome-nascent chain complex to the protein translocation machinery in the membrane. Using cryo-electron microscopy and single-particle reconstruction, we obtained a 16 Å structure of the Escherichia coli SRP in complex with a translating E. coli ribosome containing a nascent chain with a transmembrane helix anchor. We also obtained structural information on the SRP bound to an empty E. coli ribosome. The latter might share characteristics with a scanning SRP complex, whereas the former represents the next step: the targeting complex ready for receptor binding. High-resolution structures of the bacterial ribosome and of the bacterial SRP components are available, and their fitting explains our electron microscopic density. The structures reveal the regions that are involved in complex formation, provide insight into the conformation of the SRP on the ribosome and indicate the conformational changes that accompany high-affinity SRP binding to ribosome nascent chain complexes upon recognition of the signal sequence.

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: Cryo-EM structure of the RNC–SRP complex.
Figure 2: Molecular model of the SRP bound to a translating ribosome.
Figure 3: Contact sites of SRP on 50S.
Figure 4: Model of signal anchor-dependent docking of SRP to the ribosome.

Similar content being viewed by others

References

  1. Keenan, R. J., Freymann, D. M., Stroud, R. M. & Walter, P. The signal recognition particle. Annu. Rev. Biochem. 70, 755–775 (2001)

    Article  CAS  Google Scholar 

  2. Nagai, K. et al. Structure, function and evolution of the signal recognition particle. EMBO J. 22, 3479–3485 (2003)

    Article  CAS  Google Scholar 

  3. Doudna, J. A. & Batey, R. T. Structural insights into the signal recognition particle. Annu. Rev. Biochem. 73, 539–557 (2004)

    Article  CAS  Google Scholar 

  4. Ulbrandt, N. D., Newitt, J. A. & Bernstein, H. D. The E. coli signal recognition particle is required for the insertion of a subset of inner membrane proteins. Cell 88, 187–196 (1997)

    Article  CAS  Google Scholar 

  5. Walter, P. & Blobel, G. Signal recognition particle contains a 7S RNA essential for protein translocation across the endoplasmic reticulum. Nature 299, 691–698 (1982)

    Article  ADS  CAS  Google Scholar 

  6. Gu, S. Q., Peske, F., Wieden, H. J., Rodnina, M. V. & Wintermeyer, W. The signal recognition particle binds to protein L23 at the peptide exit of the Escherichia coli ribosome. RNA 9, 566–573 (2003)

    Article  CAS  Google Scholar 

  7. Pool, M. R., Stumm, J., Fulga, T. A., Sinning, I. & Dobberstein, B. Distinct modes of signal recognition particle interaction with the ribosome. Science 297, 1345–1348 (2002)

    Article  ADS  CAS  Google Scholar 

  8. Keenan, R. J., Freymann, D. M., Walter, P. & Stroud, R. M. Crystal structure of the signal sequence binding subunit of the signal recognition particle. Cell 94, 181–191 (1998)

    Article  CAS  Google Scholar 

  9. Halic, M. et al. Structure of the signal recognition particle interacting with the elongation-arrested ribosome. Nature 427, 808–814 (2004)

    Article  ADS  CAS  Google Scholar 

  10. Mitra, K. et al. Structure of the E. coli protein-conducting channel bound to a translating ribosome. Nature 438, 318–324 (2005)

    Article  ADS  CAS  Google Scholar 

  11. Valent, Q. A. et al. Nascent membrane and presecretory proteins synthesized in Escherichia coli associate with signal recognition particle and trigger factor. Mol. Microbiol. 25, 53–64 (1997)

    Article  CAS  Google Scholar 

  12. Buskiewicz, I. et al. Trigger factor binds to ribosome-signal-recognition particle (SRP) complexes and is excluded by binding of the SRP receptor. Proc. Natl Acad. Sci. USA 101, 7902–7906 (2004)

    Article  ADS  CAS  Google Scholar 

  13. Raine, A., Ivanova, N., Wikberg, J. E. & Ehrenberg, M. Simultaneous binding of trigger factor and signal recognition particle to the E. coli ribosome. Biochimie 86, 495–500 (2004)

    Article  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  15. Wriggers, W., Milligan, R. A. & McCammon, J. A. Situs: A package for docking crystal structures into low-resolution maps from electron microscopy. J. Struct. Biol. 125, 185–195 (1999)

    Article  CAS  Google Scholar 

  16. Padmanabhan, S. & Freymann, D. M. The conformation of bound GMPPNP suggests a mechanism for gating the active site of the SRP GTPase. Structure 9, 859–867 (2001)

    Article  CAS  Google Scholar 

  17. Rosendal, K. R., Wild, K., Montoya, G. & Sinning, I. Crystal structure of the complete core of archaeal signal recognition particle and implications for interdomain communication. Proc. Natl Acad. Sci. USA 100, 14701–14706 (2003)

    Article  ADS  CAS  Google Scholar 

  18. Rosenblad, M. A., Gorodkin, J., Knudsen, B., Zwieb, C. & Samuelsson, T. SRPDB: Signal Recognition Particle Database. Nucleic Acids Res. 31, 363–364 (2003)

    Article  CAS  Google Scholar 

  19. Lindahl, E., Azuara, C., Koehl, P. & Delarue, M. NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Res. 34, W52–W56 (2006)

    Article  CAS  Google Scholar 

  20. Brünger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D54, 905–921 (1998)

    Google Scholar 

  21. Wild, K., Halic, M., Sinning, I. & Beckmann, R. SRP meets the ribosome. Nature Struct. Mol. Biol. 11, 1049–1053 (2004)

    Article  CAS  Google Scholar 

  22. Ullers, R. S. et al. Interplay of signal recognition particle and trigger factor at L23 near the nascent chain exit site on the Escherichia coli ribosome. J. Cell Biol. 161, 679–684 (2003)

    Article  CAS  Google Scholar 

  23. Eisner, G., Moser, M., Schäfer, U., Beck, K. & Müller, M. Alternate recruitment of signal recognition particle and trigger factor to the signal sequence of a growing nascent polypeptide. J. Biol. Chem. 281, 7172–7179 (2006)

    Article  CAS  Google Scholar 

  24. Ferbitz, L. et al. Trigger factor in complex with the ribosome forms a molecular cradle for nascent proteins. Nature 431, 590–596 (2004)

    Article  ADS  CAS  Google Scholar 

  25. Rinke-Appel, J. et al. Crosslinking of 4.5S RNA to the Escherichia coli ribosome in the presence or absence of the protein Ffh. RNA 8, 612–625 (2002)

    Article  CAS  Google Scholar 

  26. Conway, J. F. & Steven, A. C. Methods for reconstructing density maps of “single” particles from cryoelectron micrographs to subnanometer resolution. J. Struct. Biol. 128, 106–118 (1999)

    Article  CAS  Google Scholar 

  27. 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 

  28. Valle, M. et al. Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process. EMBO J. 21, 3557–3567 (2002)

    Article  CAS  Google Scholar 

  29. Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991)

    Article  Google Scholar 

  30. Bacher, G., Lütcke, H., Jungnickel, B., Rapoport, T. A. & Dobberstein, B. Regulation by the ribosome of the GTPase of the signal-recognition particle during protein targeting. Nature 381, 248–251 (1996)

    Article  ADS  CAS  Google Scholar 

Download references

Acknowledgements

The authors would like to thank all members of the Ban laboratory for discussions and help with programs, and C. Frick, L. Verschragen (deceased) and J. Onderwater for technical assistance. W. Wintermeyer provided pET24a_Ffh. T. Shaikh and J. Frank are acknowledged for a script for supervised classification. We thank the Electron Microscopy Center Zürich (EMEZ) for support. C.S. was supported by a postdoctoral fellowship from the Ernst Schering Research Foundation. R.I.K. was supported by a VENI grant from the Netherlands Organisation for Scientific Research (NWO). This work was supported by the Swiss National Science Foundation (SNSF), the NCCR Structural Biology program of the SNSF, and a Young Investigator grant from the Human Frontier Science Program (to N.B.).

Author information

Authors and Affiliations

  1. ETH Zurich, Institute for Molecular Biology and Biophysics, HPK Building, Schafmattstrasse 20, 8093, Zurich, Switzerland

    Christiane Schaffitzel, Miro Oswald, Imre Berger, Takashi Ishikawa & Nenad Ban

  2. Department of Biophysical Structural Chemistry, Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA, Leiden, The Netherlands

    Jan Pieter Abrahams

  3. Leiden University Medical Center, Molecular Cell Biology, Center for Electron Microscopy, PO Box 9600, 2300 RC, Leiden, The Netherlands

    Henk K. Koerten & Roman I. Koning

Authors
  1. Christiane Schaffitzel
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Miro Oswald
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Imre Berger
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Takashi Ishikawa
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jan Pieter Abrahams
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Henk K. Koerten
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Roman I. Koning
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Nenad Ban
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Nenad Ban.

Ethics declarations

Competing interests

Coordinates of the atomic model of SRP have been deposited in the Protein Data Bank under the accession code 2iy3. The cryo-EM maps have been deposited in the 3D-EM database (EMBL-European Bioinformatics Institute, Cambridge, UK) under accession numbers EMD-1250 and EMD-1251. Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

Supplementary information

Supplementary Notes

This file contains the Supplementary Results and Supplementary Discussion, Supplementary Methods, Supplementary Figures and Legends 1–4, Supplementary Table 1 and additional references. (PDF 338 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Schaffitzel, C., Oswald, M., Berger, I. et al. Structure of the E. coli signal recognition particle bound to a translating ribosome. Nature 444, 503–506 (2006). https://doi.org/10.1038/nature05182

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature05182

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