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Cryo-electron tomography on focused ion beam lamellae transforms structural cell biology

Nature Methods volume 20, pages 499–511 (2023)Cite this article

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Abstract

Cryogenic electron microscopy and data processing enable the determination of structures of isolated macromolecules to near-atomic resolution. However, these data do not provide structural information in the cellular environment where macromolecules perform their native functions, and vital molecular interactions can be lost during the isolation process. Cryogenic focused ion beam (FIB) fabrication generates thin lamellae of cellular samples and tissues, enabling structural studies on the near-native cellular interior and its surroundings by cryogenic electron tomography (cryo-ET). Cellular cryo-ET benefits from the technological developments in electron microscopes, detectors and data processing, and more in situ structures are being obtained and at increasingly higher resolution. In this Review, we discuss recent studies employing cryo-ET on FIB-generated lamellae and the technological developments in ultrarapid sample freezing, FIB fabrication of lamellae, tomography, data processing and correlative light and electron microscopy that have enabled these studies. Finally, we explore the future of cryo-ET in terms of both methods development and biological application.

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Fig. 1: Overview of vitreous cryogenic sectioning and FIB fabrication of lamellae.
Fig. 2: Examples of structures obtained within cells with cryo-ET on FIB-fabricated lamellae and subsequent subtomogram averaging.
Fig. 3: Three examples of distinct applications of CLEM for cryo-ET on FIB-fabricated lamellae.

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Acknowledgements

We thank the Microscopy CORE Lab of the Maastricht MultiModal Molecular Imaging Institute of the Faculty of Health, Medicine and Life Sciences at Maastricht University for technical and scientific support. We thank M. Bárcena and S. Raunser and their co-authors for permission to modify and republish their figures. We thank H. Nguyen for editing the manuscript. We thank A. McDowall for critical reading of the manuscript. We acknowledge co-funding by the PPP Allowance made available by Health ~ Holland, Top Sector Life Sciences & Health, to stimulate public–private partnerships, under project number LHSM18067, as well as from the Netherlands Organisation for Scientific Research (NWO) in the framework of National Roadmap NEMI project number 184.034.014.

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  1. Casper Berger

    Present address: Structural Biology, The Rosalind Franklin Institute, Didcot, UK

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  1. Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands

    Casper Berger, Navya Premaraj, Raimond B. G. Ravelli, Kèvin Knoops, Carmen López-Iglesias & Peter J. Peters

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Competing interests

The University of Maastricht has filed patents, with R.B.G.R., C.L.-I. and P.J.P. as inventors, regarding vitrification devices. P.J.P. is a shareholder and chief scientific officer of the start-up CryoSol-World, which holds the licenses of these submitted patents (WO 2017/220750 and EP 3260839 B1). The other authors declare no competing interests.

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Berger, C., Premaraj, N., Ravelli, R.B.G. et al. Cryo-electron tomography on focused ion beam lamellae transforms structural cell biology. Nat Methods 20, 499–511 (2023). https://doi.org/10.1038/s41592-023-01783-5

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