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.

Structural and energetic basis of folded-protein transport by the FimD usher

Abstract

Type 1 pili, produced by uropathogenic Escherichia coli, are multisubunit fibres crucial in recognition of and adhesion to host tissues1. During pilus biogenesis, subunits are recruited to an outer membrane assembly platform, the FimD usher, which catalyses their polymerization and mediates pilus secretion2. The recent determination of the crystal structure of an initiation complex provided insight into the initiation step of pilus biogenesis resulting in pore activation, but very little is known about the elongation steps that follow3. Here, to address this question, we determine the structure of an elongation complex in which the tip complex assembly composed of FimC, FimF, FimG and FimH passes through FimD. This structure demonstrates the conformational changes required to prevent backsliding of the nascent pilus through the FimD pore and also reveals unexpected properties of the usher pore. We show that the circular binding interface between the pore lumen and the folded substrate participates in transport by defining a low-energy pathway along which the nascent pilus polymer is guided during secretion.

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

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

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

Figure 1: Structure of FimD–FimC–FimF–FimG–FimH.
Figure 2: Comparison of the structures of FimH before and after translocation.
Figure 3: Steep energy funnels and opposing binding surfaces position the translocating substrate at the centre of the pore.
Figure 4: A low-energy pathway through the pore lumen facilitates translocation of subunits and their transfer from NTD to CTDs.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

The atomic coordinates and structure factors of FimD–FimC–FimF–FimG–FimH have been deposited in the Protein Data Bank under accession ID 4J3O.

References

  1. Waksman, G. & Hultgren, S. J. Structural biology of the chaperone-usher pathway of pilus biogenesis. Nature Rev. Microbiol. 7, 765–774 (2009)

    Article  CAS  Google Scholar 

  2. Nishiyama, M., Ishikawa, T., Rechsteiner, H. & Glockshuber, R. Reconstitution of pilus assembly reveals a bacterial outer membrane catalyst. Science 320, 376–379 (2008)

    Article  ADS  CAS  Google Scholar 

  3. Phan, G. et al. Crystal structure of the FimD usher bound to its cognate FimC-FimH substrate. Nature 474, 49–53 (2011)

    Article  CAS  Google Scholar 

  4. Sauer, F. G. et al. Structural basis of chaperone function and pilus biogenesis. Science 285, 1058–1061 (1999)

    Article  CAS  Google Scholar 

  5. Sauer, F. G., Pinkner, J. S., Waksman, G. & Hultgren, S. J. Chaperone priming of pilus subunits facilitates a topological transition that drives fiber formation. Cell 111, 543–551 (2002)

    Article  CAS  Google Scholar 

  6. Choudhury, D. et al. X-ray structure of the FimC-FimH chaperone-adhesin complex from uropathogenic Escherichia coli. Science 285, 1061–1066 (1999)

    Article  CAS  Google Scholar 

  7. Zavialov, A. V. et al. Structure and biogenesis of the capsular F1 antigen from Yersinia pestis: preserved folding energy drives fiber formation. Cell 113, 587–596 (2003)

    Article  CAS  Google Scholar 

  8. Vetsch, M. et al. Pilus chaperones represent a new type of protein-folding catalyst. Nature 431, 329–333 (2004)

    Article  ADS  CAS  Google Scholar 

  9. Le Trong, I. et al. Structural basis for mechanical force regulation of the adhesin FimH via finger trap-like β-sheet twisting. Cell 141, 645–655 (2010)

    Article  CAS  Google Scholar 

  10. Das, R. & Baker, D. Macromolecular modeling with Rosetta. Annu. Rev. Biochem. 77, 363–382 (2008)

    Article  CAS  Google Scholar 

  11. Leaver-Fay, A. et al. Rosetta3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol. 487, 545–574 (2011)

    Article  CAS  Google Scholar 

  12. Huang, Y., Smith, B. S., Chen, L. X., Baxter, R. H. & Deisenhofer, J. Insights into pilus assembly and secretion from the structure and functional characterization of usher PapC. Proc. Natl Acad. Sci. USA 106, 7403–7407 (2009)

    Article  ADS  CAS  Google Scholar 

  13. Remaut, H. et al. Fiber formation across the bacterial outer membrane by the chaperone/usher pathway. Cell 133, 640–652 (2008)

    Article  CAS  Google Scholar 

  14. Kabsch, W. XDS. Acta Crystallogr. D 66, 125–132 (2010)

    Article  CAS  Google Scholar 

  15. Karplus, P. A. & Diederichs, K. Linking crystallographic model and data quality. Science 336, 1030–1033 (2012)

    Article  ADS  CAS  Google Scholar 

  16. Evans, P. Scaling and assessment of data quality. Acta Crystallogr. D 62, 72–82 (2006)

    Article  Google Scholar 

  17. McCoy, A. J. et al. PHASER crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007)

    Article  CAS  Google Scholar 

  18. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of COOT. Acta Crystallogr. D 66, 486–501 (2010)

    Article  CAS  Google Scholar 

  19. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010)

    Article  CAS  Google Scholar 

  20. Murshudov, G. N. et al. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D 67, 355–367 (2011)

    Article  CAS  Google Scholar 

  21. Schröder, G. F., Levitt, M. & Brunger, A. T. Super-resolution biomolecular crystallography with low-resolution data. Nature 464, 1218–1222 (2010)

    Article  ADS  Google Scholar 

  22. Brunger, A. T. Version 1.2 of the Crystallography and NMR system. Nature Protocols 2, 2728–2733 (2007)

    Article  CAS  Google Scholar 

  23. O’Donovan, D. J. et al. A grid-enabled web service for low-resolution crystal structure refinement. Acta Crystallogr. D 68, 261–267 (2012)

    Article  Google Scholar 

  24. DiMaio, F., Tyka, M. D., Baker, M. L., Chiu, W. & Baker, D. Refinement of protein structures into low-resolution density maps using Rosetta. J. Mol. Biol. 392, 181–190 (2009)

    Article  CAS  Google Scholar 

  25. Fleishman, S. J. et al. RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite. PLoS ONE 6, e20161 (2011)

    Article  ADS  CAS  Google Scholar 

  26. Feig, M., Karanicolas, J. & Brooks, C. L., III MMTSB tool set: enhanced sampling and multiscale modeling methods for applications in structural biology. J. Mol. Graph. Model. 22, 377–395 (2004)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was funded by Medical Research Council grant 85602 to G.W. D.B. and E.P. are supported by grant P41 GM103533 from the National Institute of General Medical Studies at the US National Institutes of Health (NIH). S.J.H. was supported by grant AI029549 from the National Institute of Allergy and Infectious Disease at the NIH. We thank the staff of beamline ID23-1 at the European Synchrotron Radiation Facility, the staff of beamline IO2 at the Diamond Light source and A. Cole for technical assistance during data collection.

Author information

Authors and Affiliations

Authors

Contributions

S.G. and E.P. carried out the crystallographic and computational work, respectively. D.B. and G.W. supervised the work. S.G., E.P., D.B. and G.W. analysed the data. S.G., E.P., S.J.H., D.B. and G.W. wrote the paper.

Corresponding authors

Correspondence to David Baker or Gabriel Waksman.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Methods, Supplementary Tables 1-2, Supplementary Figures 1-16 and Supplementary References. (PDF 23699 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Geibel, S., Procko, E., Hultgren, S. et al. Structural and energetic basis of folded-protein transport by the FimD usher. Nature 496, 243–246 (2013). https://doi.org/10.1038/nature12007

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature12007

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

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