Legionella pp 249-265 | Cite as

In Situ Imaging and Structure Determination of Bacterial Toxin Delivery Systems Using Electron Cryotomography

Part of the Methods in Molecular Biology book series (MIMB, volume 1921)


Determining the three-dimensional structure of biomacromolecules at high resolution in their native cellular environment is a major challenge for structural biology. Toward this end, electron cryotomography (ECT) allows large bio-macromolecular assemblies to be imaged directly in their hydrated physiological milieu to ~4 nm resolution. Combining ECT with other techniques like fluorescent imaging, immunogold labeling, and genetic manipulation has allowed the in situ investigation of complex biological processes at macromolecular resolution. Furthermore, the advent of cryogenic focused ion beam (FIB) milling has extended the domain of ECT to include regions even deep within thick eukaryotic cells. Anticipating two audiences (scientists who just want to understand the potential and general workflow involved and scientists who are learning how to do the work themselves), here we present both a broad overview of this kind of work and a step-by-step example protocol for ECT and subtomogram averaging using the Legionella pneumophila Dot/Icm type IV secretion system (T4SS) as a case study. While the general workflow is presented in step-by-step detail, we refer to online tutorials, user’s manuals, and other training materials for the essential background understanding needed to perform each step.

Key words

Bacterial secretion system Legionella Dot/Icm T4SS Electron cryotomography (ECT) Subtomogram averaging 



We thank Dr. Songye Chen (Caltech). This work is supported by NIH grant R01482AI127401 to G.J.J.


  1. 1.
    Sali A, Glaeser R, Earnest T, Baumeister W (2003) From words to literature in structural proteomics. Nature 422:216–225CrossRefGoogle Scholar
  2. 2.
    Robinson CV, Sali A, Baumeister W (2007) The molecular sociology of the cell. Nature 450:973–982CrossRefGoogle Scholar
  3. 3.
    Sali A, Kuriyan J (1999) Challenges at the frontiers of structural biology. Trends Cell Biol 9:M20–M24CrossRefGoogle Scholar
  4. 4.
    Baumeister W, Steven AC (2000) Macromolecular electron microscopy in the era of structural genomics. Trends Biochem Sci 25:624–631CrossRefGoogle Scholar
  5. 5.
    Curry S (2015) Structural biology: a century-long journey into an unseen world. Interdiscip Sci Rev ISR 40:308–328CrossRefGoogle Scholar
  6. 6.
    Selmer M et al (2006) Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313:1935–1942CrossRefGoogle Scholar
  7. 7.
    Wimberly BT et al (2000) Structure of the 30S ribosomal subunit. Nature 407:327–339CrossRefGoogle Scholar
  8. 8.
    Groll M et al (1997) Structure of 20S proteasome from yeast at 2.4 A resolution. Nature 386:463–471CrossRefGoogle Scholar
  9. 9.
    Abrahams JP, Leslie AG, Lutter R, Walker JE (1994) Structure at 2.8 A resolution of F1-ATPase from bovine heart mitochondria. Nature 370:621–628CrossRefGoogle Scholar
  10. 10.
    Bui KH et al (2013) Integrated structural analysis of the human nuclear pore complex scaffold. Cell 155:1233–1243CrossRefGoogle Scholar
  11. 11.
    Carter AP, Cho C, Jin L, Vale RD (2011) Crystal structure of the dynein motor domain. Science 331:1159–1165CrossRefGoogle Scholar
  12. 12.
    Vinothkumar KR, Zhu J, Hirst J (2014) Architecture of mammalian respiratory complex I. Nature 515:80–84CrossRefGoogle Scholar
  13. 13.
    Basler M, Pilhofer M, Henderson GP, Jensen GJ, Mekalanos JJ (2012) Type VI secretion requires a dynamic contractile phage tail-like structure. Nature 483:182–186CrossRefGoogle Scholar
  14. 14.
    Chang Y-W et al (2016) Architecture of the type IVa pilus machine. Science 351:aad2001CrossRefGoogle Scholar
  15. 15.
    Hu B, Lara-Tejero M, Kong Q, Galán JE, Liu J (2017) In situ molecular architecture of the salmonella type III secretion machine. Cell 168:1065–1074.e10CrossRefGoogle Scholar
  16. 16.
    Beck M, Lucić V, Förster F, Baumeister W, Medalia O (2007) Snapshots of nuclear pore complexes in action captured by cryo-electron tomography. Nature 449:611–615CrossRefGoogle Scholar
  17. 17.
    Briggs JAG (2013) Structural biology in situ—the potential of subtomogram averaging. Curr Opin Struct Biol 23:261–267CrossRefGoogle Scholar
  18. 18.
    Oikonomou CM, Jensen GJ (2017) A new view into prokaryotic cell biology from electron cryotomography. Nat Rev Microbiol 15:128CrossRefGoogle Scholar
  19. 19.
    Baumeister W (2002) Electron tomography: towards visualizing the molecular organization of the cytoplasm. Curr Opin Struct Biol 12:679–684CrossRefGoogle Scholar
  20. 20.
    Hagen WJH, Wan W, Briggs JAG (2017) Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging. J Struct Biol 197:191–198CrossRefGoogle Scholar
  21. 21.
    Grünewald K et al (2003) Three-dimensional structure of herpes simplex virus from cryo-electron tomography. Science 302:1396–1398CrossRefGoogle Scholar
  22. 22.
    Förster F, Medalia O, Zauberman N, Baumeister W, Fass D (2005) Retrovirus envelope protein complex structure in situ studied by cryo-electron tomography. Proc Natl Acad Sci U S A 102:4729–4734CrossRefGoogle Scholar
  23. 23.
    Murphy GE, Leadbetter JR, Jensen GJ (2006) In situ structure of the complete Treponema primitia flagellar motor. Nature 442:1062–1064CrossRefGoogle Scholar
  24. 24.
    Ghosal D, Chang Y-W, Jeong KC, Vogel JP, Jensen GJ (2017) In situ structure of the Legionella Dot/Icm type IV secretion system by electron cryotomography. EMBO Rep 18:726–732CrossRefGoogle Scholar
  25. 25.
    Chang YW, Shaffer CL, Rettberg LA, Ghosal D., Jensen GJ (2017) Structures of the type IV secretion system. Doi:
  26. 26.
    Chang Y, Rettberg LA, Ortega DR, Jensen GJ (2017) In vivo structures of an intact type VI secretion system revealed by electron cryotomography. EMBO Rep 18:1090–1099CrossRefGoogle Scholar
  27. 27.
    Chang Y-W et al (2017) Architecture of the Vibrio cholerae toxin-coregulated pilus machine revealed by electron cryotomography. Nat Microbiol 2:16269CrossRefGoogle Scholar
  28. 28.
    Chang Y-W et al (2014) Correlated cryogenic photoactivated localization microscopy and cryo-electron tomography. Nat Methods 11:737–739CrossRefGoogle Scholar
  29. 29.
    Kukulski W et al (2011) Correlated fluorescence and 3D electron microscopy with high sensitivity and spatial precision. J Cell Biol 192:111–119CrossRefGoogle Scholar
  30. 30.
    Danev R, Buijsse B, Khoshouei M, Plitzko JM, Baumeister W (2014) Volta potential phase plate for in-focus phase contrast transmission electron microscopy. Proc Natl Acad Sci U S A 111:15635–15640CrossRefGoogle Scholar
  31. 31.
    Campbell MG et al (2012) Movies of ice-embedded particles enhance resolution in electron cryo-microscopy. Struct. Lond. Engl 1993(20):1823–1828Google Scholar
  32. 32.
    Kühlbrandt W (2014) Biochemistry. The resolution revolution. Science 343:1443–1444CrossRefGoogle Scholar
  33. 33.
    McMullan G, Faruqi AR, Clare D, Henderson R (2014) Comparison of optimal performance at 300keV of three direct electron detectors for use in low dose electron microscopy. Ultramicroscopy 147:156–163CrossRefGoogle Scholar
  34. 34.
    Jeong KC, Ghosal D, Chang Y-W, Jensen GJ, Vogel JP (2017) Polar delivery of Legionella type IV secretion system substrates is essential for virulence. Proc Natl Acad Sci U S A 114:8077–8082CrossRefGoogle Scholar
  35. 35.
    Chen S et al (2011) Structural diversity of bacterial flagellar motors. EMBO J 30:2972–2981CrossRefGoogle Scholar
  36. 36.
    Kudryashev M et al (2013) In situ structural analysis of the Yersinia enterocolitica injectisome. elife 2:e00792CrossRefGoogle Scholar
  37. 37.
    Nans A, Kudryashev M, Saibil HR, Hayward RD (2015) Structure of a bacterial type III secretion system in contact with a host membrane in situ. Nat Commun 6:10114CrossRefGoogle Scholar
  38. 38.
    Böck D et al (2017) In situ architecture, function, and evolution of a contractile injection system. Science 357:713–717CrossRefGoogle Scholar
  39. 39.
    Yeo HJ, Savvides SN, Herr AB, Lanka E, Waksman G (2000) Crystal structure of the hexameric traffic ATPase of the Helicobacter pylori type IV secretion system. Mol Cell 6:1461–1472CrossRefGoogle Scholar
  40. 40.
    Chandran V et al (2009) Structure of the outer membrane complex of a type IV secretion system. Nature 462:1011–1015CrossRefGoogle Scholar
  41. 41.
    Gendrin C et al (2012) Structural basis of cytotoxicity mediated by the type III secretion toxin ExoU from Pseudomonas aeruginosa. PLoS Pathog 8:e1002637CrossRefGoogle Scholar
  42. 42.
    Zoued A et al (2016) Priming and polymerization of a bacterial contractile tail structure. Nature 531:59–63CrossRefGoogle Scholar
  43. 43.
    Iancu CV et al (2006) Electron cryotomography sample preparation using the Vitrobot. Nat Protoc 1:2813–2819CrossRefGoogle Scholar
  44. 44.
    Fullner KJ, Lara JC, Nester EW (1996) Pilus assembly by Agrobacterium T-DNA transfer genes. Science 273:1107–1109CrossRefGoogle Scholar
  45. 45.
    Tivol WF, Briegel A, Jensen GJ (2008) An improved cryogen for plunge freezing. Microsc Microanal 14:375–379CrossRefGoogle Scholar
  46. 46.
    Suloway C et al (2005) Automated molecular microscopy: the new Leginon system. J Struct Biol 151:41–60CrossRefGoogle Scholar
  47. 47.
    Mastronarde DN (2005) Automated electron microscope tomography using robust prediction of specimen movements. J Struct Biol 152:36–51CrossRefGoogle Scholar
  48. 48.
    Zheng SQ et al (2007) UCSF tomography: an integrated software suite for real-time electron microscopic tomographic data collection, alignment, and reconstruction. J Struct Biol 157:138–147CrossRefGoogle Scholar
  49. 49.
    Zheng SQ et al (2017) MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat Methods 14:331–332CrossRefGoogle Scholar
  50. 50.
    Kremer JR, Mastronarde DN, McIntosh JR (1996) Computer visualization of three-dimensional image data using IMOD. J Struct Biol 116:71–76CrossRefGoogle Scholar
  51. 51.
    Mastronarde DN (2008) Correction for non-perpendicularity of beam and tilt axis in tomographic reconstructions with the IMOD package. J Microsc 230:212–217CrossRefGoogle Scholar
  52. 52.
    Agulleiro J-I, Fernandez J-J (2015) Tomo3D 2.0—exploitation of advanced vector extensions (AVX) for 3D reconstruction. J Struct Biol 189:147–152CrossRefGoogle Scholar
  53. 53.
    Nicastro D et al (2006) The molecular architecture of axonemes revealed by cryoelectron tomography. Science 313:944–948CrossRefGoogle Scholar
  54. 54.
    Hrabe T et al (2012) PyTom: a python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis. J Struct Biol 178:177–188CrossRefGoogle Scholar
  55. 55.
    Bharat TAM, Scheres SHW (2016) Resolving macromolecular structures from electron cryo-tomography data using subtomogram averaging in RELION. Nat Protoc 11:2054–2065CrossRefGoogle Scholar
  56. 56.
    Castaño-Díez D, Kudryashev M, Arheit M, Stahlberg H (2012) Dynamo: a flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments. J Struct Biol 178:139–151CrossRefGoogle Scholar
  57. 57.
    Pettersen EF et al (2004) UCSF Chimera—a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612CrossRefGoogle Scholar
  58. 58.
    Kucukelbir A, Sigworth FJ, Tagare HD (2014) Quantifying the local resolution of cryo-EM density maps. Nat Methods 11:63–65CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUSA
  2. 2.Howard Hughes Medical InstitutePasadenaUSA

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