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

Nature volume 444, pages 503506 (23 November 2006) | Download Citation

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  • 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.

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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

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

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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.

Corresponding author

Correspondence to Nenad Ban.

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    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.

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https://doi.org/10.1038/nature05182

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