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Atomic model of the type III secretion system needle

Nature volume 486, pages 276–279 (2012)Cite this article

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A Corrigendum to this article was published on 08 August 2012

Abstract

Pathogenic bacteria using a type III secretion system (T3SS)1,2 to manipulate host cells cause many different infections including Shigella dysentery, typhoid fever, enterohaemorrhagic colitis and bubonic plague. An essential part of the T3SS is a hollow needle-like protein filament through which effector proteins are injected into eukaryotic host cells3,4,5,6. Currently, the three-dimensional structure of the needle is unknown because it is not amenable to X-ray crystallography and solution NMR, as a result of its inherent non-crystallinity and insolubility. Cryo-electron microscopy combined with crystal or solution NMR subunit structures has recently provided a powerful hybrid approach for studying supramolecular assemblies7,8,9,10,11,12, resulting in low-resolution and medium-resolution models13,14,15,16,17. However, such approaches cannot deliver atomic details, especially of the crucial subunit–subunit interfaces, because of the limited cryo-electron microscopic resolution obtained in these studies. Here we report an alternative approach combining recombinant wild-type needle production, solid-state NMR, electron microscopy and Rosetta modelling to reveal the supramolecular interfaces and ultimately the complete atomic structure of the Salmonella typhimurium T3SS needle. We show that the 80-residue subunits form a right-handed helical assembly with roughly 11 subunits per two turns, similar to that of the flagellar filament of S. typhimurium. In contrast to established models of the needle in which the amino terminus of the protein subunit was assumed to be α-helical and positioned inside the needle, our model reveals an extended amino-terminal domain that is positioned on the surface of the needle, while the highly conserved carboxy terminus points towards the lumen.

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Figure 1: Structural data from ssNMR.
Figure 2: Architecture of the T3SS needle assembly as determined by ssNMR.
Figure 3: Complete atomic model of the T3SS needle.

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Accession codes

Primary accessions

Protein Data Bank

Data deposits

The Salmonella typhimurium T3SS PrgI needle structure is deposited in the Protein Data Bank under the accession code 2LPZ.

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Acknowledgements

We thank T. C. Marlovits and E. H. Egelman for providing the S. typhimurium T3SS needle cryo-electron microscopy density map; F. DiMaio and J.-P. Demers for discussions; and G. Wolf, B. Angerstein and G. Heim for technical help. This work was supported by the Max Planck Society (to C. Griesinger), the Deutsche Forschungsgemeinschaft (Emmy Noether Fellowship to A. Lange), the Fondation Bettencourt Schueller (to A. Loquet), the National Institutes of Health (1 R01 GM092802-01 to D.B.), EMBO (postdoctoral fellowship to A. Loquet), and the European Union Seventh Framework Program under Grant Agreement 261863 (Bio-NMR).

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Author notes

  1. Antoine Loquet, Nikolaos G. Sgourakis, Rashmi Gupta and Karin Giller: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany,

    Antoine Loquet, Karin Giller, Christian Griesinger, Stefan Becker & Adam Lange

  2. Department of Biochemistry, University of Washington, Seattle, 98195, Washington, USA

    Nikolaos G. Sgourakis & David Baker

  3. Department of Cellular Microbiology, Max Planck Institute for Infection Biology, 10117 Berlin, Germany,

    Rashmi Gupta & Michael Kolbe

  4. Laboratory for Electron Microscopy, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany,

    Dietmar Riedel

  5. Core Facility Microscopy, Max Planck Institute for Infection Biology, 10117 Berlin, Germany,

    Christian Goosmann

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  1. Antoine Loquet
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Contributions

A. Loquet performed ssNMR experiments. A. Loquet and A. Lange analysed ssNMR data. N.S. and D.B. performed structure calculations. K.G. and S.B. expressed, purified and polymerized in vitro T3SS needles. R.G. and M.K. performed the in vivo studies. C. Griesinger analysed NMR data. D.R. and C. Goosmann performed electron microscopy studies. A. Loquet and A. Lange wrote the paper; all authors discussed the results and commented on the manuscript.

Corresponding authors

Correspondence to Michael Kolbe, Stefan Becker or Adam Lange.

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The authors declare no competing financial interests.

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This file contains Supplementary Figures 1-18, Supplementary Tables 1-3 and Supplementary References. (PDF 7243 kb)

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Loquet, A., Sgourakis, N., Gupta, R. et al. Atomic model of the type III secretion system needle. Nature 486, 276–279 (2012). https://doi.org/10.1038/nature11079

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