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Structure of the signal recognition particle interacting with the elongation-arrested ribosome

Nature volume 427, pages 808–814 (2004)Cite this article

Abstract

Cotranslational translocation of proteins across or into membranes is a vital process in all kingdoms of life. It requires that the translating ribosome be targeted to the membrane by the signal recognition particle (SRP), an evolutionarily conserved ribonucleoprotein particle. SRP recognizes signal sequences of nascent protein chains emerging from the ribosome. Subsequent binding of SRP leads to a pause in peptide elongation and to the ribosome docking to the membrane-bound SRP receptor. Here we present the structure of a targeting complex consisting of mammalian SRP bound to an active 80S ribosome carrying a signal sequence. This structure, solved to 12 Å by cryo-electron microscopy, enables us to generate a molecular model of SRP in its functional conformation. The model shows how the S domain of SRP contacts the large ribosomal subunit at the nascent chain exit site to bind the signal sequence, and that the Alu domain reaches into the elongation-factor-binding site of the ribosome, explaining its elongation arrest activity.

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Figure 1: Cryo-EM map of mammalian SRP bound to 80S RNC at 12.0 Å.
Figure 2: Molecular model of SRP.
Figure 3: Interaction of the SRP S domain with the 80S ribosome.
Figure 4: Interaction of the SRP Alu domain with the 80S ribosome.
Figure 5: Signal-sequence-dependent SRP–ribosome interaction.

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References

  1. Blobel, G. & Sabatini, D. in Biomembranes (ed. Manson, L. A.) 193–195 (Plenum, New York, 1971)

    Book  Google Scholar 

  2. Walter, P., Ibrahimi, I. & Blobel, G. Translocation of proteins across the endoplasmic reticulum. I. Signal recognition protein (SRP) binds to in-vitro-assembled polysomes synthesizing secretory protein. J. Cell Biol. 91, 545–550 (1981)

    Article  CAS  Google Scholar 

  3. Koch, H. G., Moser, M. & Muller, M. Signal recognition particle-dependent protein targeting, universal to all kingdoms of life. Rev. Physiol. Biochem. Pharmacol. 146, 55–94 (2003)

    Article  CAS  Google Scholar 

  4. Gundelfinger, E. D., Krause, E., Melli, M. & Dobberstein, B. The organization of the 7SL RNA in the signal recognition particle. Nucleic Acids Res. 11, 7363–7374 (1983)

    Article  CAS  Google Scholar 

  5. Siegel, V. & Walter, P. Each of the activities of signal recognition particle (SRP) is contained within a distinct domain: analysis of biochemical mutants of SRP. Cell 52, 39–49 (1988)

    Article  CAS  Google Scholar 

  6. Walter, P. & Blobel, G. Disassembly and reconstitution of signal recognition particle. Cell 34, 525–533 (1983)

    Article  CAS  Google Scholar 

  7. Connolly, T. & Gilmore, R. The signal recognition particle receptor mediates the GTP-dependent displacement of SRP from the signal sequence of the nascent polypeptide. Cell 57, 599–610 (1989)

    Article  CAS  Google Scholar 

  8. Bernstein, H. D. et al. Model for signal sequence recognition from amino-acid sequence of 54K subunit of signal recognition particle. Nature 340, 482–486 (1989)

    Article  ADS  CAS  Google Scholar 

  9. Romisch, K., Webb, J., Lingelbach, K., Gausepohl, H. & Dobberstein, B. The 54-kD protein of signal recognition particle contains a methionine-rich RNA binding domain. J. Cell Biol. 111, 1793–1802 (1990)

    Article  CAS  Google Scholar 

  10. Batey, R. T., Rambo, R. P., Lucast, L., Rha, B. & Doudna, J. A. Crystal structure of the ribonucleoprotein core of the signal recognition particle. Science 287, 1232–1239 (2000)

    Article  ADS  CAS  Google Scholar 

  11. Zopf, D., Bernstein, H. D., Johnson, A. E. & Walter, P. The methionine-rich domain of the 54 kD protein subunit of the signal recognition particle contains an RNA binding site and can be crosslinked to a signal sequence. EMBO J. 9, 4511–4517 (1990)

    Article  CAS  Google Scholar 

  12. 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 

  13. Siegel, V. & Walter, P. Removal of the Alu structural domain from signal recognition particle leaves its protein translocation activity intact. Nature 320, 81–84 (1986)

    Article  ADS  CAS  Google Scholar 

  14. Walter, P. & Blobel, G. Translocation of proteins across the endoplasmic reticulum. III. Signal recognition protein (SRP) causes signal sequence-dependent and site-specific arrest of chain elongation that is released by microsomal membranes. J. Cell Biol. 91, 557–561 (1981)

    Article  CAS  Google Scholar 

  15. Wolin, S. L. & Walter, P. Signal recognition particle mediates a transient elongation arrest of preprolactin in reticulocyte lysate. J. Cell Biol. 109, 2617–2622 (1989)

    Article  CAS  Google Scholar 

  16. Mason, N., Ciufo, L. F. & Brown, J. D. Elongation arrest is a physiologically important function of signal recognition particle. EMBO J. 19, 4164–4174 (2000)

    Article  CAS  Google Scholar 

  17. Siegel, V. & Walter, P. Elongation arrest is not a prerequisite for secretory protein translocation across the microsomal membrane. J. Cell Biol. 100, 1913–1921 (1985)

    Article  CAS  Google Scholar 

  18. Andrews, D. W., Walter, P. & Ottensmeyer, F. P. Evidence for an extended 7SL RNA structure in the signal recognition particle. EMBO J. 6, 3471–3477 (1987)

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  20. Beckmann, R. et al. Architecture of the protein-conducting channel associated with the translating 80S ribosome. Cell 107, 361–372 (2001)

    Article  CAS  Google Scholar 

  21. Walter, P. & Blobel, G. Subcellular distribution of signal recognition particle and 7SL-RNA determined with polypeptide-specific antibodies and complementary DNA probe. J. Cell Biol. 97, 1693–1699 (1983)

    Article  CAS  Google Scholar 

  22. Spahn, C. M. et al. Structure of the 80S ribosome from Saccharomyces cerevisiae tRNA–ribosome and subunit–subunit interactions. Cell 107, 373–386 (2001)

    Article  CAS  Google Scholar 

  23. Kuglstatter, A., Oubridge, C. & Nagai, K. Induced structural changes of 7SL RNA during the assembly of human signal recognition particle. Nature Struct. Biol. 9, 740–744 (2002)

    Article  CAS  Google Scholar 

  24. Huang, Q., Abdulrahman, S., Yin, J. & Zwieb, C. Systematic site-directed mutagenesis of human protein SRP54: interactions with signal recognition particle RNA and modes of signal peptide recognition. Biochemistry 41, 11362–11371 (2002)

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  26. 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 

  27. Siegel, V. & Walter, P. Binding sites of the 19-kDa and 68/72-kDa signal recognition particle (SRP) proteins on SRP RNA as determined in protein–RNA ‘footprinting’. Proc. Natl Acad. Sci. USA 85, 1801–1805 (1988)

    Article  ADS  CAS  Google Scholar 

  28. Ban, N., Nissen, P., Hansen, J., Moore, P. B. & Steitz, T. A. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289, 905–920 (2000)

    Article  ADS  CAS  Google Scholar 

  29. Weichenrieder, O., Wild, K., Strub, K. & Cusack, S. Structure and assembly of the Alu domain of the mammalian signal recognition particle. Nature 408, 167–173 (2000)

    Article  ADS  CAS  Google Scholar 

  30. 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 

  31. 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 

  32. Eisner, G., Koch, H. G., Beck, K., Brunner, J. & Muller, M. Ligand crowding at a nascent signal sequence. J. Cell Biol. 163, 35–44 (2003)

    Article  CAS  Google Scholar 

  33. Kramer, G. et al. L23 protein functions as a chaperone docking site on the ribosome. Nature 419, 171–174 (2002)

    Article  ADS  CAS  Google Scholar 

  34. 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 

  35. 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 

  36. Morgan, D. G., Menetret, J. F., Neuhof, A., Rapoport, T. A. & Akey, C. W. Structure of the mammalian ribosome–channel complex at 17 Å resolution. J. Mol. Biol. 324, 871–886 (2002)

    Article  CAS  Google Scholar 

  37. Moller, I. et al. A general mechanism for regulation of access to the translocon: competition for a membrane attachment site on ribosomes. Proc. Natl Acad. Sci. USA 95, 13425–13430 (1998)

    Article  ADS  CAS  Google Scholar 

  38. Thomas, Y., Bui, N. & Strub, K. A truncation in the 14 kDa protein of the signal recognition particle leads to tertiary structure changes in the RNA and abolishes the elongation arrest activity of the particle. Nucleic Acids Res. 25, 1920–1929 (1997)

    Article  CAS  Google Scholar 

  39. Wilson, D. N. et al. Protein synthesis at atomic resolution: mechanistics of translation in the light of highly resolved structures for the ribosome. Curr. Protein Peptide Sci. 3, 1–53 (2002)

    Article  CAS  Google Scholar 

  40. Gomez-Lorenzo, M. G. et al. Three-dimensional cryo-electron microscopy localization of EF2 in the Saccharomyces cerevisiae 80S ribosome at 17.5 Å resolution. EMBO J. 19, 2710–2718 (2000)

    Article  CAS  Google Scholar 

  41. Spahn, C. et al. Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation. EMBO J. (in the press)

  42. Valle, M. et al. Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy. Nature Struct. Biol. 10, 899–906 (2003)

    Article  CAS  Google Scholar 

  43. Wolin, S. L. & Walter, P. Ribosome pausing and stacking during translation of a eukaryotic mRNA. EMBO J. 7, 3559–3569 (1988)

    Article  CAS  Google Scholar 

  44. Ogg, S. C. & Walter, P. SRP samples nascent chains for the presence of signal sequences by interacting with ribosomes at a discrete step during translation elongation. Cell 81, 1075–1084 (1995)

    Article  CAS  Google Scholar 

  45. Andreazzoli, M. & Gerbi, S. A. Changes in 7SL RNA conformation during the signal recognition particle cycle. EMBO J. 10, 767–777 (1991)

    Article  CAS  Google Scholar 

  46. Martoglio, B., Hauser, S. & Dobberstein, B. in Cell Biology: A Laboratory Handbook (ed. Celis, J. C.) 265–273 (Academic, San Diego, 1997)

    Google Scholar 

  47. Walter, P. & Blobel, G. Signal recognition particle: a ribonucleoprotein required for cotranslational translocation of proteins, isolation and properties. Methods Enzymol. 96, 682–691 (1983)

    Article  CAS  Google Scholar 

  48. Wagenknecht, T., Grassucci, R. & Frank, J. Electron microscopy and computer image averaging of ice-embedded large ribosomal subunits from Escherichia coli. J. Mol. Biol. 199, 137–147 (1988)

    Article  CAS  Google Scholar 

  49. Jones, T. A., Zhou, 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 

  50. Carson, M. Ribbons 2.0. Appl. Crystallogr. 24, 103–106 (1991)

    Article  Google Scholar 

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Acknowledgements

We thank C. Böttcher for help with the F20 cryo-microscope; U. Bach for technical assistance; and B. Dobberstein for support. This work was supported by a grant of the VolkswagenStiftung (to R.B.), by grants from NIH, NSF and HHMI (to J.F.) and by the European Union and the Senatsverwaltung für Wissenschaft, Forschung und Kultur Berlin in the context of the Ultra-Structure Network.

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Authors and Affiliations

  1. Institute of Biochemistry, Charité, University Medical School, Humboldt University of Berlin, Monbijoustrasse 2, 10117, Berlin, Germany

    Mario Halic, Thomas Becker & Roland Beckmann

  2. University of Manchester, School of Biological Sciences, 2.205 Stopford Building, Oxford Road, Manchester, M13 9PT, UK

    Martin R. Pool

  3. Institute of Medical Physics and Biophysics, Charité, University Medical School, Humboldt University of Berlin, Ziegelstrasse 9, 10117, Berlin, Germany

    Christian M. T. Spahn

  4. Howard Hughes Medical Institute, Health Research Incorporated, Wadsworth Center, Empire State Plaza, Albany, New York, 12201

    Robert A. Grassucci & Joachim Frank

  5. Department of Biomedical Sciences, State University of New York at Albany, Albany, New York, 12222, USA

    Robert A. Grassucci & Joachim Frank

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Correspondence to Roland Beckmann.

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Supplementary information

Supplementary Figure 1

Purification of RNCs and reconstitution of the RNC-SRP complex. (JPG 43 kb)

Supplementary Figure 2

Cryo-EM map and resolution of the SRP-RNC complex. (JPG 93 kb)

Supplementary Movie 1

Animated cryo-EM structure of RNC-SRP complex as shown in Fig. 1. (MPG 3035 kb)

Supplementary Movie 2

Animated molecular model of mammalian SRP as shown in Fig. 2. (MPG 2941 kb)

Supplementary Figure and Movie Legends (DOC 20 kb)

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Halic, M., Becker, T., Pool, M. et al. Structure of the signal recognition particle interacting with the elongation-arrested ribosome. Nature 427, 808–814 (2004). https://doi.org/10.1038/nature02342

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