Hostname: page-component-745bb68f8f-b95js Total loading time: 0 Render date: 2025-02-04T16:58:36.306Z Has data issue: false hasContentIssue false

Structural biology inside multicellular specimens using electron cryotomography

Published online by Cambridge University Press:  13 January 2025

Ido Caspy
Affiliation:
Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK
Zhexin Wang
Affiliation:
Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK
Tanmay A.M. Bharat*
Affiliation:
Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK
*
Corresponding author: Tanmay A.M. Bharat; Email: tbharat@mrc-lmb.cam.ac.uk

Abstract

The electron cryomicroscopy (cryo-EM) resolution revolution has shifted structural biology into a new era, enabling the routine structure determination of macromolecular complexes at an unprecedented rate. Building on this, electron cryotomography (cryo-ET) offers the potential to visualise the native three-dimensional organisation of biological specimens, from cells to tissues and even entire organisms. Despite this huge potential, the study of tissue-like multicellular specimens via cryo-ET still presents numerous challenges, wherein many steps in the workflow are being developed or in urgent need of improvement. In this review, we outline the latest techniques currently utilised for in situ imaging of multicellular specimens, while clearly enumerating their associated limitations. We consider every step in typical workflows employed by various laboratories, including sample preparation, data collection and image analysis, to highlight recent progress and showcase prominent success stories. By considering the entire structural biology workflow for multicellular specimens, we identify which future exciting developments in hardware and software could enable comprehensive in situ structural biology investigations, bringing forth a new age of discovery in molecular structural and cell biology.

Type
Review
Copyright
© MRC Laboratory of Molecular Biology, 2025. Published by Cambridge University Press

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Al-Amoudi, A, Norlen, LPO and Dubochet, J (2004) Cryo-electron microscopy of vitreous sections of native biological cells and tissues. Journal of Structural Biology 148(1), 131135. https://doi.org/10.1016/J.JSB.2004.03.010CrossRefGoogle ScholarPubMed
Al-Amoudi, A, Studer, D and Dubochet, J (2005) Cutting artefacts and cutting process in vitreous sections for cryo-electron microscopy. Journal of Structural Biology 150(1), 109121. https://doi.org/10.1016/J.JSB.2005.01.003CrossRefGoogle ScholarPubMed
Allegretti, M, Zimmerli, CE, Rantos, V, Wilfling, F, Ronchi, P, Fung, HKH, Lee, CW, Hagen, W, Turoňová, B, Karius, K, Börmel, M, Zhang, X, Müller, CW, Schwab, Y, Mahamid, J, Pfander, B, Kosinski, J and Beck, M (2020) In-cell architecture of the nuclear pore and snapshots of its turnover. Nature 586(7831), 796800. https://doi.org/10.1038/s41586-020-2670-5CrossRefGoogle ScholarPubMed
Axelrod, JJ, Petrov, PN, Zhang, JT, Remis, J, Buijsse, B, Glaeser, RM and Mȕller, H (2023) Overcoming resolution loss due to thermal magnetic field fluctuations from phase plates in transmission electron microscopy. Ultramicroscopy 249, 113730. https://doi.org/10.1016/J.ULTRAMIC.2023.113730CrossRefGoogle ScholarPubMed
Axelrod, JJ, Petrov, PN, Zhang, JT, Sandhaus, S, Remis, J, Glaeser, RM and Müller, H (2023) Overcoming resolution loss in laser phase plate cryo-electron microscopy. Microscopy and Microanalysis 29(Supplement_1), 10171017. https://doi.org/10.1093/MICMIC/OZAD067.513CrossRefGoogle Scholar
Bäuerlein, FJB, Renner, M, Chami, DEl, Lehnart, SE, Pastor-Pareja, JC and Fernández-Busnadiego, R (2023) Cryo-electron tomography of large biological specimens vitrified by plunge freezing. BioRxiv, 2021.04.14.437159. https://doi.org/10.1101/2021.04.14.437159CrossRefGoogle Scholar
Baumeister, W (2005) From proteomic inventory to architecture. FEBS Letters 579(4), 933937. https://doi.org/10.1016/J.FEBSLET.2004.10.102CrossRefGoogle ScholarPubMed
Baumeister, W, Grimm, R and Walz, J (1999) Electron tomography of molecules and cells. Trends in Cell Biology 9(2), 8185. https://doi.org/10.1016/S0962-8924(98)01423-8CrossRefGoogle ScholarPubMed
Beck, M and Baumeister, W (2016) Cryo-electron tomography: Can it reveal the molecular sociology of cells in atomic detail? Trends in Cell Biology 26(11), 825837. https://doi.org/10.1016/J.TCB.2016.08.006CrossRefGoogle ScholarPubMed
Berger, C, Dumoux, M, Glen, T, Yee, NBy., Mitchels, JM, Patáková, Z, Darrow, MC, Naismith, JH and Grange, M (2023) Plasma FIB milling for the determination of structures in situ. Nature Communications 14(1), 112. https://doi.org/10.1038/s41467-023-36372-9CrossRefGoogle ScholarPubMed
Berger, C, Premaraj, N, Ravelli, RBG, Knoops, K, López-Iglesias, C and Peters, PJ (2023) Cryo-electron tomography on focused ion beam lamellae transforms structural cell biology. Nature Methods 20(4), 499511. https://doi.org/10.1038/s41592-023-01783-5CrossRefGoogle ScholarPubMed
Berger, C, Watson, H, Naismith, J, Dumoux, M and Grange, M (2024) Xenon plasma focused ion beam lamella fabrication on high-pressure frozen specimens for structural cell biology. BioRxiv, 2024.06.20.599830. https://doi.org/10.1101/2024.06.20.599830CrossRefGoogle Scholar
Bharat, TAM, Hoffmann, PC and Kukulski, W (2018) Correlative microscopy of vitreous sections provides insights into BAR-domain organization in situ. Structure 26(6), 879886.e3. https://doi.org/10.1016/J.STR.2018.03.015CrossRefGoogle ScholarPubMed
Bharat, T.AM, Russo, CJ, Löwe, J, Passmore, LA and Scheres, SHW (2015) Advances in single-particle electron cryomicroscopy structure determination applied to sub-tomogram averaging. Structure 23(9), 1743. https://doi.org/10.1016/J.STR.2015.06.026CrossRefGoogle ScholarPubMed
Bock, LV and Grubmüller, H (2022) Effects of cryo-EM cooling on structural ensembles. Nature Communications 13(1), 113. https://doi.org/10.1038/s41467-022-29332-2CrossRefGoogle ScholarPubMed
Böhning, J and Bharat, TAM (2021) Towards high-throughput in situ structural biology using electron cryotomography. Progress in Biophysics and Molecular Biology 160, 97103. https://doi.org/10.1016/J.PBIOMOLBIO.2020.05.010CrossRefGoogle ScholarPubMed
Bouvette, J, Liu, HF, Du, X, Zhou, Y, Sikkema, AP, da Fonseca Rezende e Mello, J, Klemm, BP, Huang, R, Schaaper, RM, Borgnia, MJ and Bartesaghi, A (2021) Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography. Nature Communications 12(1), 111. https://doi.org/10.1038/s41467-021-22251-8CrossRefGoogle ScholarPubMed
Briggs, JAG (2013) Structural biology in situ--The potential of subtomogram averaging. Current Opinion in Structural Biology 23(2), 261267. https://doi.org/10.1016/J.SBI.2013.02.003CrossRefGoogle ScholarPubMed
Brown, HG, Smith, D, Wardle, BC and Hanssen, E (2024) Square condenser apertures for square cameras in low-dose transmission electron microscopy. Nature Methods 21(4), 566568. https://doi.org/10.1038/s41592-024-02206-9CrossRefGoogle ScholarPubMed
Buchholz, TO, Jordan, M, Pigino, G and Jug, F (2018) Cryo-CARE: Content-aware image restoration for cryo-transmission electron microscopy data. In Proceedings - International Symposium on Biomedical Imaging, 2019 April, 502506. https://doi.org/10.1109/ISBI.2019.8759519CrossRefGoogle Scholar
Burnett, TL, Kelley, R, Winiarski, B, Contreras, L, Daly, M, Gholinia, A, Burke, MG and Withers, PJ (2016) Large volume serial section tomography by Xe plasma FIB dual beam microscopy. Ultramicroscopy 161, 119129. https://doi.org/10.1016/J.ULTRAMIC.2015.11.001CrossRefGoogle ScholarPubMed
Burt, A, Toader, B, Warshamanage, R, von Kügelgen, A, Pyle, E, Zivanov, J, Kimanius, D, Bharat, TAM and Scheres, SHW (2024) An image processing pipeline for electron cryo-tomography in RELION-5. FEBS Open Bio. https://doi.org/10.1002/2211-5463.13873CrossRefGoogle Scholar
Campbell, SL, Schwartz, O, Axelrod, JJ, Turnbaugh, C, Glaeser, RM and Müller, H (2018) A laser-based phase plate for phase contrast transmission electron microscopy. Frontiers in Optics/Laser Science, Part F114-FIO 2018, FW7B.5. https://doi.org/10.1364/FIO.2018.FW7B.5CrossRefGoogle Scholar
Capua-Shenkar, J, Varsano, N, Itzhak, NR, Kaplan-Ashiri, I, Rechav, K, Jin, X, Niimi, M, Fan, J, Kruth, HS and Addadi, L (2022) Examining atherosclerotic lesions in three dimensions at the nanometer scale with cryo-FIB-SEM. Proceedings of the National Academy of Sciences of the United States of America 119(34), e2205475119. https://doi.org/10.1073/PNAS.2205475119CrossRefGoogle ScholarPubMed
Carzaniga, R, Domart, MC, Collinson, LM and Duke, E (2014) Cryo-soft X-ray tomography: A journey into the world of the native-state cell. Protoplasma 251(2), 449458. https://doi.org/10.1007/S00709-013-0583-YCrossRefGoogle ScholarPubMed
Chaillet, ML, Roet, S, Veltkamp, RC and Förster, F (2024) Pytom-match-pick: A Tophat-transform constraint for automated classification in template matching. BioRxiv, 2024.09.17.613497. https://doi.org/10.1101/2024.09.17.613497CrossRefGoogle Scholar
Chang, IY, Rahman, M, Harned, A, Cohen-Fix, O and Narayan, K (2021) Cryo-fluorescence microscopy of high-pressure frozen C. elegans enables correlative FIB-SEM imaging of targeted embryonic stages in the intact worm. Methods in Cell Biology 162, 223. https://doi.org/10.1016/BS.MCB.2020.09.009CrossRefGoogle ScholarPubMed
Chang, Y, Lu, W, Guénolé, J, Stephenson, LT, Szczpaniak, A, Kontis, P, Ackerman, AK, Dear, FF, Mouton, I, Zhong, X, Zhang, S, Dye, D, Liebscher, CH, Ponge, D, Korte-Kerzel, S, Raabe, D and Gault, B (2019) Ti and its alloys as examples of cryogenic focused ion beam milling of environmentally-sensitive materials. Nature Communications 10(1), 110. https://doi.org/10.1038/s41467-019-08752-7CrossRefGoogle ScholarPubMed
Chen, M, Bell, JM, Shi, X, Sun, SY, Wang, Z and Ludtke, SJ (2019) A complete data processing workflow for cryo-ET and subtomogram averaging. Nature Methods 16(11), 11611168. https://doi.org/10.1038/s41592-019-0591-8CrossRefGoogle ScholarPubMed
Chen, S, Basiashvili, T, Hutchings, J, Murillo, MS, Suarez, AV, Louro, JA, Leschziner, AE and Villa, E (2024) Cryo-electron tomography reveals the microtubule-bound form of inactive LRRK2. ELife 13. https://doi.org/10.7554/ELIFE.100799.1Google Scholar
Chen, Z, Shiozaki, M, Haas, KM, Skinner, WM, Zhao, S, Guo, C, Polacco, BJ, Yu, Z, Krogan, NJ, Lishko, PV, Kaake, RM, Vale, RD and Agard, DA (2023) De novo protein identification in mammalian sperm using in situ cryoelectron tomography and AlphaFold2 docking. Cell 186(23), 50415053.e19. https://doi.org/10.1016/J.CELL.2023.09.017CrossRefGoogle ScholarPubMed
Chreifi, G, Chen, S and Jensen, GJ (2021) Rapid tilt-series method for cryo-electron tomography: Characterizing stage behavior during FISE acquisition. Journal of Structural Biology 213(2), 107716. https://doi.org/10.1016/J.JSB.2021.107716CrossRefGoogle ScholarPubMed
Chreifi, G, Chen, S, Metskas, LA, Kaplan, M and Jensen, GJ (2019) Rapid tilt-series acquisition for electron cryotomography. Journal of Structural Biology 205(2), 163169. https://doi.org/10.1016/J.JSB.2018.12.008CrossRefGoogle ScholarPubMed
Chua, EYD, Alink, LM, Kopylov, M, Johnston, JD, Eisenstein, F and de Marco, A (2024) Square beams for optimal tiling in transmission electron microscopy. Nature Methods 21(4), 562565. https://doi.org/10.1038/s41592-023-02161-xCrossRefGoogle ScholarPubMed
Cleeve, P, Caggiano, MP, Dierickx, D, Whisstock, J and de Marco, A (2023) Automation in Cryo-FIB preparation, from cellular to tissue structural biology. Microscopy and Microanalysis 29(29 Suppl 1), 1956. https://doi.org/10.1093/MICMIC/OZAD067.1013CrossRefGoogle Scholar
Creekmore, BC, Kixmoeller, K, Black, BE, Lee, EB and Chang, YW (2024) Ultrastructure of human brain tissue vitrified from autopsy revealed by cryo-ET with cryo-plasma FIB milling. Nature Communications 15(1), 112. https://doi.org/10.1038/s41467-024-47066-1CrossRefGoogle ScholarPubMed
Cruz-León, S, Majtner, T, Hoffmann, PC, Kreysing, JP, Kehl, S, Tuijtel, MW, Schaefer, SL, Geißler, K, Beck, M, Turoňová, B and Hummer, G (2024) High-confidence 3D template matching for cryo-electron tomography. Nature Communications 15(1), 114. https://doi.org/10.1038/s41467-024-47839-8CrossRefGoogle ScholarPubMed
Dahl, R and Staehelin, LA (1989) Highpressure freezing for the preservation of biological structure: Theory and practice. Journal of Electron Microscopy Technique 13(3), 165174. https://doi.org/10.1002/JEMT.1060130305CrossRefGoogle ScholarPubMed
Dandey, VP, Budell, WC, Wei, H, Bobe, D, Maruthi, K, Kopylov, M, Eng, ET, Kahn, PA, Hinshaw, JE, Kundu, N, Nimigean, CM, Fan, C, Sukomon, N, Darst, SA, Saecker, RM, Chen, J, Malone, B, Potter, CS and Carragher, B (2020) Time-resolved cryo-EM using Spotiton. Nature Methods 17(9), 897900. https://doi.org/10.1038/s41592-020-0925-6CrossRefGoogle ScholarPubMed
De Rosier, DJ and Klug, A (1968) Reconstruction of three dimensional structures from electron micrographs. Nature 217(5124), 130134. https://doi.org/10.1038/217130a0CrossRefGoogle ScholarPubMed
de Teresa-Trueba, I, Goetz, SK, Mattausch, A, Stojanovska, F, Zimmerli, CE, Toro-Nahuelpan, M, Cheng, DWC, Tollervey, F, Pape, C, Beck, M, Diz-Muñoz, A, Kreshuk, A, Mahamid, J and Zaugg, JB (2023) Convolutional networks for supervised mining of molecular patterns within cellular context. Nature Methods 20(2), 284294. https://doi.org/10.1038/s41592-022-01746-2CrossRefGoogle ScholarPubMed
Denk, W and Horstmann, H (2004) Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLoS Biology 2(11) https://doi.org/10.1371/journal.pbio.0020329CrossRefGoogle ScholarPubMed
D’Imprima, E, Garcia Montero, M, Gawrzak, S, Ronchi, P, Zagoriy, I, Schwab, Y, Jechlinger, M and Mahamid, J (2023) Light and electron microscopy continuum-resolution imaging of 3D cell cultures. Developmental Cell 58(7), 616632.e6. https://doi.org/10.1016/J.DEVCEL.2023.03.001CrossRefGoogle ScholarPubMed
Du, DX and Fitzpatrick, AWP (2023) Design of an ultrafast pulsed ponderomotive phase plate for cryo-electron tomography. Cell Reports Methods 3(1), 100387. https://doi.org/10.1016/J.CRMETH.2022.100387CrossRefGoogle ScholarPubMed
Dubochet, J, Adrian, M, Chang, J-J, Homo, J-C, Lepault, J, McDowall, AW and Schultz, P (1988) Cryo-electron microscopy of vitrified specimens. Quarterly Reviews of Biophysics 21(2), 129228. https://doi.org/10.1017/S0033583500004297CrossRefGoogle ScholarPubMed
Dubochet, J and McDowall, AW (1981) Vitrification of pure water for electron microscopy. Journal of Microscopy 124(3), 34. https://doi.org/10.1111/J.1365-2818.1981.TB02483.XCrossRefGoogle Scholar
Dumoux, M, Glen, T, Smith, JL, Ho, EM, Perdigão, LM, Pennington, A, Klumpe, S, Yee, NB, Farmer, DA, Lai, PY, Bowles, W, Kelley, R, Plitzko, JM, Wu, L, Basham, M, Clare, DK, Siebert, CA, Darrow, MC, Naismith, JH and Grange, M (2023) Cryo-plasma FIB/SEM volume imaging of biological specimens. ELife 12. https://doi.org/10.7554/ELIFE.83623CrossRefGoogle ScholarPubMed
Eder, K, Bhatia, V, Qu, J, Van Leer, B, Dutka, M and Cairney, JM (2021) A multi-ion plasma FIB study: Determining ion implantation depths of Xe, N, O and Ar in tungsten via atom probe tomography. Ultramicroscopy 228, 113334. https://doi.org/10.1016/J.ULTRAMIC.2021.113334CrossRefGoogle Scholar
Eisenstein, F, Danev, R and Pilhofer, M (2019) Improved applicability and robustness of fast cryo-electron tomography data acquisition. Journal of Structural Biology 208(2), 107114. https://doi.org/10.1016/J.JSB.2019.08.006CrossRefGoogle ScholarPubMed
Eisenstein, F, Fukuda, Y and Danev, R (2023) Smart parallel automated cryo electron tomography. BioRxiv, 2023.12.14.571776. https://doi.org/10.1101/2023.12.14.571776CrossRefGoogle Scholar
Eisenstein, F, Yanagisawa, H, Kashihara, H, Kikkawa, M, Tsukita, S and Danev, R (2022) Parallel cryo electron tomography on in situ lamellae. Nature Methods 20(1), 131138. https://doi.org/10.1038/s41592-022-01690-1CrossRefGoogle ScholarPubMed
Elad, N, Bellapadrona, G, Houben, L, Sagi, I and Elbaum, M (2017) Detection of isolated protein-bound metal ions by single-particle cryo-STEM. Proceedings of the National Academy of Sciences of the United States of America 114(42), 1113911144. https://doi.org/10.1073/pnas.1708609114CrossRefGoogle ScholarPubMed
Elbaum, M (2018) Expanding horizons of cryo-tomography to larger volumes. Current Opinion in Microbiology 43, 155161. https://doi.org/10.1016/J.MIB.2018.01.001CrossRefGoogle ScholarPubMed
Elbaum, M, Seifer, S, Houben, L, Wolf, SG and Rez, P (2021) Toward compositional contrast by cryo-STEM. Accounts of Chemical Research 54(19), 36213631. https://doi.org/10.1021/ACS.ACCOUNTS.1C00279CrossRefGoogle ScholarPubMed
Eltsov, M, Grewe, D, Lemercier, N, Frangakis, A, Livolant, F and Leforestier, A (2018) Nucleosome conformational variability in solution and in interphase nuclei evidenced by cryo-electron microscopy of vitreous sections. Nucleic Acids Research 46(17), 91899200. https://doi.org/10.1093/NAR/GKY670CrossRefGoogle ScholarPubMed
Esser, TK, Böhning, J, Önür, A, Chinthapalli, DK, Eriksson, L, Grabarics, M, Fremdling, P, Konijnenberg, A, Makarov, A, Botman, A, Peter, C, Benesch, JLP., Robinson, CV, Gault, J, Baker, L, Bharat, TAM. and Rauschenbach, S (2024) Cryo-EM of soft-landed β-galactosidase: Gas-phase and native structures are remarkably similar. Science Advances 10(7), 4628. https://doi.org/10.1126/SCIADV.ADL4628CrossRefGoogle ScholarPubMed
Fahy, K, Kapishnikov, S, Donnellan, M, McEnroe, T, O’Reilly, F, Fyans, W and Sheridan, P (2024) Laboratory based correlative cryo-soft X-ray tomography and cryo-fluorescence microscopy. Methods in Cell Biology 187, 293320. https://doi.org/10.1016/BS.MCB.2024.02.033CrossRefGoogle ScholarPubMed
Fahy, K, Weinhardt, V, Vihinen-Ranta, M, Fletcher, N, Skoko, D, Pereiro, E, Gastaminza, P, Bartenschlager, R, Scholz, D, Ekman, A and McEnroe, T (2021) Compact cell imaging device (CoCID) provides insights into the cellular origins of viral infections. Journal of Physics: Photonics 3(3), 031002. https://doi.org/10.1088/2515-7647/ABFC5AGoogle Scholar
Fedry, J, Silva, J, Vanevic, M, Fronik, S, Mechulam, Y, Schmitt, E, des Georges, A, Faller, WJ and Förster, F (2024) Visualization of translation reorganization upon persistent ribosome collision stress in mammalian cells. Molecular Cell 84(6), 10781089.e4. https://doi.org/10.1016/J.MOLCEL.2024.01.015CrossRefGoogle ScholarPubMed
Förster, F, Medalia, O, Zauberman, N, Baumeister, W and Fass, D (2005) Retrovirus envelope protein complex structure in situ studied by cryo-electron tomography. Proceedings of the National Academy of Sciences of the United States of America 102(13), 47294734. https://doi.org/10.1073/PNAS.0409178102CrossRefGoogle ScholarPubMed
Frank, J (1995) Approaches to large-scale structures. Current Opinion in Structural Biology 5(2), 194201. https://doi.org/10.1016/0959-440X(95)80075-1CrossRefGoogle ScholarPubMed
Fuest, M, Schaffer, M, Nocera, GM, Galilea-Kleinsteuber, RI, Messling, JE, Heymann, M, Plitzko, JM and Burg, TP (2019) In situ microfluidic cryofixation for cryo focused ion beam milling and cryo electron tomography. Scientific Reports 9(1), 110. https://doi.org/10.1038/s41598-019-55413-2CrossRefGoogle ScholarPubMed
Gan, L and Jensen, GJ (2012) Electron tomography of cells. Quarterly Reviews of Biophysics 45(1), 2756. https://doi.org/10.1017/S0033583511000102CrossRefGoogle ScholarPubMed
Gemmer, M, Chaillet, ML, van Loenhout, J, Cuevas Arenas, R, Vismpas, D, Gröllers-Mulderij, M, Koh, FA, Albanese, P, Scheltema, RA, Howes, SC, Kotecha, A, Fedry, J and Förster, F (2023) Visualization of translation and protein biogenesis at the ER membrane. Nature 614(7946), 160167. https://doi.org/10.1038/s41586-022-05638-5CrossRefGoogle ScholarPubMed
Gilbert, MAG, Fatima, N, Jenkins, J, O’Sullivan, TJ, Schertel, A, Halfon, Y, Wilkinson, M, Morrema, THJ, Geibel, M, Read, RJ, Ranson, NA, Radford, SE, Hoozemans, JJM and Frank, RAW (2024) CryoET of β-amyloid and tau within postmortem Alzheimer’s disease brain. Nature 631(8022), 913919. https://doi.org/10.1038/s41586-024-07680-xCrossRefGoogle ScholarPubMed
Gorelick, S and De Marco, A (2018) Fabrication of glass microlenses using focused Xe beam. Optics Express 26(10), 1364713655. https://doi.org/10.1364/OE.26.013647CrossRefGoogle ScholarPubMed
Guo, J and Larabell, CA (2019) Soft X-ray tomography: Virtual sculptures from cell cultures. Current Opinion in Structural Biology 58, 324332. https://doi.org/10.1016/J.SBI.2019.06.012CrossRefGoogle ScholarPubMed
Guo, Q, Lehmer, C, Martínez-Sánchez, A, Rudack, T, Beck, F, Hartmann, H, Pérez-Berlanga, M, Frottin, F, Hipp, MS, Hartl, FU, Edbauer, D, Baumeister, W and Fernández-Busnadiego, R (2018) In situ structure of neuronal C9orf72 poly-GA aggregates reveals proteasome recruitment. Cell 172(4), 696705.e12. https://doi.org/10.1016/J.CELL.2017.12.030CrossRefGoogle ScholarPubMed
Harapin, J, Börmel, M, Sapra, KT, Brunner, D, Kaech, A and Medalia, O (2015) Structural analysis of multicellular organisms with cryo-electron tomography. Nature Methods 12(7), 634636. https://doi.org/10.1038/nmeth.3401CrossRefGoogle ScholarPubMed
Held, RG, Liang, J and Brunger, AT (2024) Nanoscale architecture of synaptic vesicles and scaffolding complexes revealed by cryo-electron tomography. Proceedings of the National Academy of Sciences of the United States of America 121(27), e2403136121. https://doi.org/10.1073/PNAS.2403136121CrossRefGoogle ScholarPubMed
Henderson, R (1992) Image contrast in high-resolution electron microscopy of biological macromolecules: TMV in ice. Ultramicroscopy 46(1–4), 118. https://doi.org/10.1016/0304-3991(92)90003-3CrossRefGoogle ScholarPubMed
Henderson, R (2004) Realizing the potential of electron cryo-microscopy. Quarterly Reviews of Biophysics 37(1), 313. https://doi.org/10.1017/S0033583504003920CrossRefGoogle ScholarPubMed
Heymann, JAW, Hayles, M, Gestmann, I, Giannuzzi, LA, Lich, B and Subramaniam, S (2006) Site-specific 3D imaging of cells and tissues with a dual beam microscope. Journal of Structural Biology 155(1), 6373. https://doi.org/10.1016/J.JSB.2006.03.006CrossRefGoogle ScholarPubMed
Himes, BA and Zhang, P (2018) emClarity: Software for high-resolution cryo-electron tomography and subtomogram averaging. Nature Methods 15(11), 955961. https://doi.org/10.1038/s41592-018-0167-zCrossRefGoogle ScholarPubMed
Hoffmann, PC, Kreysing, JP, Khusainov, I, Tuijtel, MW, Welsch, S and Beck, M (2022) Structures of the eukaryotic ribosome and its translational states in situ. Nature Communications 13(1), 19. https://doi.org/10.1038/s41467-022-34997-wCrossRefGoogle ScholarPubMed
Hoppe, W (1970) Principles of electron structure research at atomic resolution using conventional electron microscopes for the measurement of amplitudes and phases. Acta Cryst 26, 414.CrossRefGoogle Scholar
Hoppe, W (1974) Towards three-dimensional “electron microscopy” at atomic resolution. Die Naturwissenschaften 61(6), 239249. https://doi.org/10.1007/BF00595655CrossRefGoogle ScholarPubMed
Hutchings, J, Stancheva, V, Miller, EA and Zanetti, G (2018) Subtomogram averaging of COPII assemblies reveals how coat organization dictates membrane shape. Nature Communications 9(1) https://doi.org/10.1038/S41467-018-06577-4CrossRefGoogle ScholarPubMed
Hutchings, J and Zanetti, G (2018) Fine details in complex environments: The power of cryo-electron tomography. Biochemical Society Transactions 46(4), 807. https://doi.org/10.1042/BST20170351CrossRefGoogle ScholarPubMed
Iulianella, A (2017) Cutting thick sections using a vibratome. Cold Spring Harbor Protocols 2017(6), 505508. https://doi.org/10.1101/PDB.PROT094011CrossRefGoogle ScholarPubMed
Jentoft, IMA, Bäuerlein, FJB, Welp, LM, Cooper, BH, Petrovic, A, So, C, Penir, SM, Politi, AZ, Horokhovskyi, Y, Takala, I, Eckel, H, Moltrecht, R, Lénárt, P, Cavazza, T, Liepe, J, Brose, N, Urlaub, H, Fernández-Busnadiego, R and Schuh, M (2023) Mammalian oocytes store proteins for the early embryo on cytoplasmic lattices. Cell 186(24), 53085327.e25. https://doi.org/10.1016/J.CELL.2023.10.003CrossRefGoogle ScholarPubMed
Jones, AV and Leonard, KR (1978) Scanning transmission electron microscopy of unstained biological sections. Nature 271(5646), 659660. https://doi.org/10.1038/271659a0CrossRefGoogle ScholarPubMed
Jumper, J, Evans, R, Pritzel, A, Green, T, Figurnov, M, Ronneberger, O, Tunyasuvunakool, K, Bates, R, Žídek, A, Potapenko, A, Bridgland, A, Meyer, C, Kohl, SAA, Ballard, AJ, Cowie, A, Romera-Paredes, B, Nikolov, S, Jain, R, Adler, J, … Hassabis, D (2021) Highly accurate protein structure prediction with AlphaFold. Nature 596(7873), 583589. https://doi.org/10.1038/s41586-021-03819-2CrossRefGoogle ScholarPubMed
Kellenberger, E, Carlemalm, E, Villiger, W, Wurtz, M, Mory, C and Colliex, C (1986) Z-contrast in biology: A comparison with other imaging modes. Annals of the New York Academy of Sciences 483(1), 202228. https://doi.org/10.1111/J.1749-6632.1986.TB34522.XCrossRefGoogle ScholarPubMed
Kelley, K, Raczkowski, AM, Klykov, O, Jaroenlak, P, Bobe, D, Kopylov, M, Eng, ET, Bhabha, G, Potter, CS, Carragher, B and Noble, AJ (2022) Waffle method: A general and flexible approach for improving throughput in FIB-milling. Nature Communications 13(1), 113. https://doi.org/10.1038/s41467-022-29501-3CrossRefGoogle Scholar
Kirchweger, P, Mullick, D, Wolf, SG and Elbaum, M (2023) Visualization of organelles in situ by cryo-STEM tomography. Journal of Visualized Experiments (JoVE) 2023(196), e65052. https://doi.org/10.3791/65052Google Scholar
Klumpe, S, Fung, HKH, Goetz, SK, Zagoriy, I, Hampoelz, B, Zhang, X, Erdmann, PS, Baumbach, J, Müller, CW, Beck, M, Plitzko, JM and Mahamid, J (2021) A modular platform for automated cryo-FIB Workflows. ELife 10. https://doi.org/10.7554/ELIFE.70506CrossRefGoogle ScholarPubMed
Klumpe, S, Kuba, J, Schioetz, OH, Erdmann, PS, Rigort, A and Plitzko, JM (2022) Recent advances in gas injection system-free cryo-FIB lift-out transfer for cryo-electron tomography of multicellular organisms and tissues. Microscopy Today 30(1), 4247. https://doi.org/10.1017/S1551929521001528CrossRefGoogle Scholar
Klumpe, S, Schioetz, OH, Kaiser, C, Luchner, M, Brenner, J and Plitzko, JM (2023) Developments in cryo-FIB sample preparation: Targeting in cryo-lift-out preparation of tissues and machine learning models for fully automated on-grid lamella preparation. Microscopy and Microanalysis 29(Supplement_1), 511513. https://doi.org/10.1093/MICMIC/OZAD067.243CrossRefGoogle Scholar
Koeck, PJB and Karshikoff, A (2015) Limitations of the linear and the projection approximations in three-dimensional transmission electron microscopy of fully hydrated proteins. Journal of Microscopy 259(3), 197209. https://doi.org/10.1111/JMI.12253CrossRefGoogle ScholarPubMed
Kravčenko, U, Ruwolt, M, Kroll, J, Yushkevich, A, Zenkner, M, Ruta, J, Lotfy, R, Wanker, EE, Rosenmund, C, Liu, F and Kudryashev, M (2024) Molecular architecture of synaptic vesicles. Proceedings of the National Academy of Sciences of the United States of America 121(49), e2407375121. https://doi.org/10.1073/PNAS.2407375121CrossRefGoogle ScholarPubMed
Kremer, JR, Mastronarde, DN and McIntosh, JR (1996) Computer visualization of three-dimensional image data using IMOD. Journal of Structural Biology 116(1), 7176. https://doi.org/10.1006/JSBI.1996.0013CrossRefGoogle ScholarPubMed
Kuba, J, Mitchels, J, Hovorka, M, Erdmann, P, Berka, L, Kirmse, R, König, J, De Bock, J, Goetze, B and Rigort, A (2021) Advanced cryo-tomography workflow developments – correlative microscopy, milling automation and cryo-lift-out. Journal of Microscopy 281(2), 112124. https://doi.org/10.1111/JMI.12939CrossRefGoogle ScholarPubMed
Kühlbrandt, W (2014) The resolution revolution. Science 343(6178), 14431444. https://doi.org/10.1126/science.1251652CrossRefGoogle ScholarPubMed
Lai, WC, Lin, CY, Chang, WT, Li, PC, Fu, TY, Chang, CS, Tsong, TT and Hwang, IS (2017) Xenon gas field ion source from a single-atom tip. Nanotechnology 28(25), 255301. https://doi.org/10.1088/1361-6528/AA6ED3CrossRefGoogle ScholarPubMed
Lam, V and Villa, E (2021) Practical approaches for cryo-FIB milling and applications for cellular cryo-electron tomography. Methods in Molecular Biology 2215, 4982. https://doi.org/10.1007/978-1-0716-0966-8_3CrossRefGoogle Scholar
Larabell, CA and Le Gros, MA (2004) X-ray tomography generates 3-D reconstructions of the yeast, Saccharomyces cerevisiae, at 60-nm resolution. Molecular Biology of the Cell 15(3), 957. https://doi.org/10.1091/MBC.E03-07-0522CrossRefGoogle ScholarPubMed
Larabell, CA and Nugent, KA (2010) Imaging cellular architecture with X-rays. Current Opinion in Structural Biology 20(5), 623. https://doi.org/10.1016/J.SBI.2010.08.008CrossRefGoogle ScholarPubMed
Lazić, I, Wirix, M, Leidl, ML, de Haas, F, Mann, D, Beckers, M, Pechnikova, EV, Müller-Caspary, K, Egoavil, R, Bosch, EGT and Sachse, C (2022) Single-particle cryo-EM structures from iDPC–STEM at near-atomic resolution. Nature Methods 19(9), 11261136. https://doi.org/10.1038/s41592-022-01586-0CrossRefGoogle ScholarPubMed
Leistner, C, Wilkinson, M, Burgess, A, Lovatt, M, Goodbody, S, Xu, Y, Deuchars, S, Radford, SE, Ranson, NA and Frank, RAW (2023) The in-tissue molecular architecture of β-amyloid pathology in the mammalian brain. Nature Communications 14(1), 112. https://doi.org/10.1038/s41467-023-38495-5CrossRefGoogle ScholarPubMed
Leung, MR, Zeng, J, Wang, X, Roelofs, MC, Huang, W, Zenezini Chiozzi, R, Hevler, JF, Heck, AJR, Dutcher, SK, Brown, A, Zhang, R and Zeev-Ben-Mordehai, T (2023) Structural specializations of the sperm tail. Cell 186(13), 28802896.e17. https://doi.org/10.1016/j.cell.2023.05.026CrossRefGoogle ScholarPubMed
Lindell, AE, Grießhammer, A, Michaelis, L, Papagiannidis, D, Ochner, H, Kamrad, S, Guan, R, Blasche, S, Ventimiglia, L, Ramachandran, B, Ozgur, H, Zelezniak, A, Beristain-Covarrubias, N, Yam-Puc, JC, Roux, I, Barron, LP, Richardson, AK, Martin, MG, Benes, V, … Patil, KR (2024) Extensive PFAS accumulation by human gut bacteria. BioRxiv, 2024.09.17.613493. https://doi.org/10.1101/2024.09.17.613493CrossRefGoogle Scholar
Liu, HF, Zhou, Y, Huang, Q, Piland, J, Jin, W, Mandel, J, Du, X, Martin, J and Bartesaghi, A (2023) nextPYP: A comprehensive and scalable platform for characterizing protein variability in situ using single-particle cryo-electron tomography. Nature Methods 20(12), 19091919. https://doi.org/10.1038/s41592-023-02045-0CrossRefGoogle ScholarPubMed
Liu, YT, Zhang, H, Wang, H, Tao, CL, Bi, GQ and Zhou, ZH (2022) Isotropic reconstruction for electron tomography with deep learning. Nature Communications 13(1), 117. https://doi.org/10.1038/s41467-022-33957-8Google ScholarPubMed
Lucas, BA and Grigorieff, N (2023) Quantification of gallium cryo-FIB milling damage in biological lamellae. Proceedings of the National Academy of Sciences of the United States of America 120(23), e2301852120. https://doi.org/10.1073/PNAS.2301852120CrossRefGoogle ScholarPubMed
Lucas, BA, Himes, BA and Grigorieff, N (2023) Baited reconstruction with 2D template matching for high-resolution structure determination in vitro and in vivo without template bias. ELife, 12. https://doi.org/10.7554/ELIFE.90486.2CrossRefGoogle ScholarPubMed
Lučić, V, Rigort, A and Baumeister, W (2013) Cryo-electron tomography: The challenge of doing structural biology in situ. Journal of Cell Biology 202(3), 407419. https://doi.org/10.1083/JCB.201304193CrossRefGoogle ScholarPubMed
Ma, OX, Chong, WG, Lee, JKE, Cai, S, Siebert, CA, Howe, A, Zhang, P, Shi, J, Surana, U and Gan, L (2022) Cryo-ET detects bundled triple helices but not ladders in meiotic budding yeast. PLOS ONE 17(4), e0266035. https://doi.org/10.1371/JOURNAL.PONE.0266035CrossRefGoogle Scholar
Mahamid, J, Pfeffer, S, Schaffer, M, Villa, E, Danev, R, Cuellar, LK, Förster, F, Hyman, AA, Plitzko, JM and Baumeister, W (2016) Visualizing the molecular sociology at the HeLa cell nuclear periphery. Science 351(6276), 969972. https://doi.org/10.1126/SCIENCE.AAD8857CrossRefGoogle ScholarPubMed
Mahamid, J, Schampers, R, Persoon, H, Hyman, AA, Baumeister, W and Plitzko, JM (2015) A focused ion beam milling and lift-out approach for site-specific preparation of frozen-hydrated lamellas from multicellular organisms. Journal of Structural Biology 192(2), 262269. https://doi.org/10.1016/J.JSB.2015.07.012CrossRefGoogle ScholarPubMed
Marko, M, Hsieh, C, Moberlychan, W, Mannella, CA and Frank, J (2006) Focused ion beam milling of vitreous water: Prospects for an alternative to cryo-ultramicrotomy of frozen-hydrated biological samples. Journal of Microscopy 222(1), 4247. https://doi.org/10.1111/J.1365-2818.2006.01567.XCrossRefGoogle ScholarPubMed
Marko, M, Hsieh, C, Schalek, R, Frank, J and Mannella, C (2007) Focused-ion-beam thinning of frozen-hydrated biological specimens for cryo-electron microscopy. Nature Methods 4(3), 215217. https://doi.org/10.1038/nmeth1014CrossRefGoogle ScholarPubMed
Mastronarde, DN (2005) Automated electron microscope tomography using robust prediction of specimen movements. Journal of Structural Biology 152(1), 3651. https://doi.org/10.1016/J.JSB.2005.07.007CrossRefGoogle ScholarPubMed
Matsui, A, Spangler, CJ, Elferich, J, Shiozaki, M, Jean, N, Zhao, X, Qin, M, Zhong, H, Yu, Z and Gouaux, E (2024) Cryo-electron tomographic investigation of native hippocampal glutamatergic synapses. ELife 13. https://doi.org/10.7554/ELIFE.98458.2CrossRefGoogle ScholarPubMed
Mattei, S, Glass, B, Hagen, WJH, Kräusslich, HG and Briggs, JAG (2016) The structure and flexibility of conical HIV-1 capsids determined within intact virions. Science 354(6318), 14341437. https://doi.org/10.1126/SCIENCE.AAH4972CrossRefGoogle ScholarPubMed
McCafferty, CL, Klumpe, S, Amaro, RE, Kukulski, W, Collinson, L and Engel, BD (2024) Integrating cellular electron microscopy with multimodal data to explore biology across space and time. Cell 187(3), 563584. https://doi.org/10.1016/J.CELL.2024.01.005CrossRefGoogle ScholarPubMed
McDonald, K, Schwarz, H, Müller-Reichert, T, Webb, R, Buser, C and Morphew, M (2010) “Tips and tricks” for high-pressure freezing of model systems. Methods in Cell Biology 96(C), 671693. https://doi.org/10.1016/S0091-679X(10)96028-7CrossRefGoogle ScholarPubMed
McDowall, AW, Chang, J-J, Freeman, R, Lepault, J, Walter, CA and Dubochet, J (1983) Electron microscopy of frozen hydrated sections of vitreous ice and vitrified biological samples. Journal of Microscopy 131(1), 19. https://doi.org/10.1111/J.1365-2818.1983.TB04225.XCrossRefGoogle ScholarPubMed
Medeiros, JM, Böck, D, Weiss, GL, Kooger, R, Wepf, RA and Pilhofer, M (2018) Robust workflow and instrumentation for cryo-focused ion beam milling of samples for electron cryotomography. Ultramicroscopy 190, 111. https://doi.org/10.1016/J.ULTRAMIC.2018.04.002CrossRefGoogle ScholarPubMed
Melia, CE and Bharat, TAM (2018) Locating macromolecules and determining structures inside bacterial cells using electron cryotomography. Biochimica et Biophysica Acta 1866(9), 973. https://doi.org/10.1016/J.BBAPAP.2018.06.003CrossRefGoogle ScholarPubMed
Moebel, E, Martinez-Sanchez, A, Lamm, L, Righetto, RD, Wietrzynski, W, Albert, S, Larivière, D, Fourmentin, E, Pfeffer, S, Ortiz, J, Baumeister, W, Peng, T, Engel, BD and Kervrann, C (2021) Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms. Nature Methods 18(11), 13861394. https://doi.org/10.1038/s41592-021-01275-4CrossRefGoogle ScholarPubMed
Moor, H (1987) Theory and practice of high pressure freezing. Cryotechniques in Biological Electron Microscopy, 175191. https://doi.org/10.1007/978-3-642-72815-0_8CrossRefGoogle Scholar
Moor, H and Riehle, U (1968) Snap-freezing under high pressure: a new fixation technique for freeze-etching. In Bocciarelli, S (ed.), Proceedings of 4th European Regional Conference on Electron Microscopy, 3334.Google Scholar
Müller, H, Jin, J, Danev, R, Spence, J, Padmore, H and Glaeser, RM (2010) Design of an electron microscope phase plate using a focused continuous-wave laser. New Journal of Physics 12. https://doi.org/10.1088/1367-2630/12/7/073011CrossRefGoogle ScholarPubMed
Neselu, K, Wang, B, Rice, WJ, Potter, CS, Carragher, B and Chua, EYD (2023) Measuring the effects of ice thickness on resolution in single particle cryo-EM. Journal of Structural Biology X 7, 100085. https://doi.org/10.1016/J.YJSBX.2023.100085CrossRefGoogle ScholarPubMed
Nguyen, HTD, Perone, G, Klena, N, Vazzana, R, Kaluthantrige Don, F, Silva, M, Sorrentino, S, Swuec, P, Leroux, F, Kalebic, N, Coscia, F and Erdmann, PS (2024) Serialized on-grid lift-in sectioning for tomography (SOLIST) enables a biopsy at the nanoscale. Nature Methods 21(9), 16931701. https://doi.org/10.1038/s41592-024-02384-6CrossRefGoogle ScholarPubMed
Ni, T, Sun, Y, Burn, W, Al-Hazeem, MMJ, Zhu, Y, Yu, X, Liu, LN and Zhang, P (2022) Structure and assembly of cargo Rubisco in two native α-carboxysomes. Nature Communications 13(1), 19. https://doi.org/10.1038/s41467-022-32004-wCrossRefGoogle ScholarPubMed
Noble, AJ and de Marco, A (2024) Cryo-focused ion beam for in situ structural biology: State of the art, challenges, and perspectives. Current Opinion in Structural Biology 87. https://doi.org/10.1016/J.SBI.2024.102864CrossRefGoogle ScholarPubMed
Nogales, E and Mahamid, J (2024) Bridging structural and cell biology with cryo-electron microscopy. Nature 628(8006), 4756. https://doi.org/10.1038/s41586-024-07198-2CrossRefGoogle ScholarPubMed
Nogales, E and Scheres, SHW (2015) Cryo-EM: A unique tool for the visualization of macromolecular complexity. Molecular Cell 58(4), 677689. https://doi.org/10.1016/J.MOLCEL.2015.02.019CrossRefGoogle ScholarPubMed
Obr, M, Keizer, J, Righetto, R, Zhang, X, Kelley, R, Khavnekar, S, Franken, E, Engel, B, Plitzko, J and Kotecha, A (2024) Cryo-electron tomography of Chlamydomonas reinhardtii: Leveraging electron event representation (EER) image format in visual proteomics. Microscopy and Microanalysis 30(Supplement_1). https://doi.org/10.1093/MAM/OZAE044.363CrossRefGoogle Scholar
Ochner, H and Bharat, TAM (2023) Charting the molecular landscape of the cell. Structure, 31(11) 12971305. https://doi.org/10.1016/J.STR.2023.08.015CrossRefGoogle ScholarPubMed
Oikonomou, CM, Chang, YW and Jensen, GJ (2016) A new view into prokaryotic cell biology from electron cryotomography. Nature Reviews Microbiology 14(4), 205220. https://doi.org/10.1038/NRMICRO.2016.7CrossRefGoogle ScholarPubMed
O’Reilly, FJ, Xue, L, Graziadei, A, Sinn, L, Lenz, S, Tegunov, D, Blötz, C, Singh, N, Hagen, WJH, Cramer, P, Stülke, J, Mahamid, J and Rappsilber, J (2020) In-cell architecture of an actively transcribing-translating expressome. Science 369(6503), 554. https://doi.org/10.1126/SCIENCE.ABB3758CrossRefGoogle ScholarPubMed
Otón, J, Pereiro, E, Conesa, JJ, Chichón, FJ, Luque, D, Rodríguez, JM, Pérez-Berná, AJ, Sorzano, COS, Klukowska, J, Herman, GT, Vargas, J, Marabini, R, Carrascosa, JL and Carazo, JM (2017) XTEND: Extending the depth of field in cryo soft X-ray tomography. Scientific Reports 7(1), 112. https://doi.org/10.1038/srep45808CrossRefGoogle ScholarPubMed
Parkhurst, JM, Crawshaw, AD, Siebert, CA, Dumoux, M, Owen, CD, Nunes, P, Waterman, D, Glen, T, Stuart, DI, Naismith, JH and Evans, G (2023) Investigation of the milling characteristics of different focused-ion-beam sources assessed by three-dimensional electron diffraction from crystal lamellae. IUCrJ 10(Pt 3), 270287. https://doi.org/10.1107/S2052252523001902CrossRefGoogle ScholarPubMed
Passarelli, MK, Pirkl, A, Moellers, R, Grinfeld, D, Kollmer, F, Havelund, R, Newman, CF, Marshall, PS, Arlinghaus, H, Alexander, MR, West, A, Horning, S, Niehuis, E, Makarov, A, Dollery, CT and Gilmore, IS (2017) The 3D OrbiSIMS—Label-free metabolic imaging with subcellular lateral resolution and high mass-resolving power. Nature Methods 14(12), 11751183. https://doi.org/10.1038/nmeth.4504CrossRefGoogle ScholarPubMed
Peck, A, Carter, SD, Mai, H, Chen, S, Burt, A and Jensen, GJ (2022) Montage electron tomography of vitrified specimens. Journal of Structural Biology 214(2), 107860. https://doi.org/10.1016/J.JSB.2022.107860CrossRefGoogle ScholarPubMed
Pegg, DE (2007) Principles of cryopreservation. Methods in Molecular Biology 368, 3957. https://doi.org/10.1007/978-1-59745-362-2_3CrossRefGoogle ScholarPubMed
Petrov, PN, Müller, H and Glaeser, RM (2022) Perspective: Emerging strategies for determining atomic-resolution structures of macromolecular complexes within cells. Journal of Structural Biology 214(1), 107827. https://doi.org/10.1016/J.JSB.2021.107827CrossRefGoogle ScholarPubMed
Plitzko, JM, Klumpe, S, Schioetz, OH, Bieber, A, Capitanio, C, Kuba, J and Rigort, A (2022) On the road to correlative cryo-lift-out, fully automated waffles and beyond – Make the most out of your tissue sample. Microscopy and Microanalysis 28(S1), 12921295. https://doi.org/10.1017/S143192762200530XCrossRefGoogle Scholar
Pyle, E, Miller, EA and Zanetti, G (2024) Cryo-electron tomography reveals how COPII assembles on cargo-containing membranes. Nature Structural & Molecular Biology, 17. https://doi.org/10.1038/s41594-024-01413-4CrossRefGoogle Scholar
Ravelli, RBG, Nijpels, FJT, Henderikx, RJM, Weissenberger, G, Thewessem, S, Gijsbers, A, Beulen, BWAMM, López-Iglesias, C and Peters, PJ (2020) Cryo-EM structures from sub-nl volumes using pin-printing and jet vitrification. Nature Communications 11(1), 19. https://doi.org/10.1038/s41467-020-16392-5CrossRefGoogle ScholarPubMed
Rice, G, Wagner, T, Stabrin, M, Sitsel, O, Prumbaum, D and Raunser, S (2023) TomoTwin: Generalized 3D localization of macromolecules in cryo-electron tomograms with structural data mining. Nature Methods 20(6), 871880. https://doi.org/10.1038/S41592-023-01878-ZCrossRefGoogle ScholarPubMed
Rigort, A, Bäuerlein, FJB, Villa, E, Eibauer, M, Laugks, T, Baumeister, W and Plitzko, JM (2012) Focused ion beam micromachining of eukaryotic cells for cryoelectron tomography. Proceedings of the National Academy of Sciences of the United States of America 109(12), 44494454. https://doi.org/10.1073/PNAS.1201333109CrossRefGoogle ScholarPubMed
Rigort, A and Plitzko, JM (2015) Cryo-focused-ion-beam applications in structural biology. Archives of Biochemistry and Biophysics 581, 122130. https://doi.org/10.1016/J.ABB.2015.02.009CrossRefGoogle ScholarPubMed
Rigort, A, Villa, E, Bäuerlein, FJB, Engel, BD and Plitzko, JM (2012) Integrative approaches for cellular cryo-electron tomography: Correlative imaging and focused ion beam micromachining. Methods in Cell Biology 111, 259281. https://doi.org/10.1016/B978-0-12-416026-2.00014-5CrossRefGoogle ScholarPubMed
Rubino, S, Akhtar, S, Melin, P, Searle, A, Spellward, P and Leifer, K (2012) A site-specific focused-ion-beam lift-out method for cryo transmission electron microscopy. Journal of Structural Biology 180(3), 572576. https://doi.org/10.1016/J.JSB.2012.08.012CrossRefGoogle ScholarPubMed
dos Santos, Á, Knowles, O, Dendooven, T, Hale, T, Hale, VL, Burt, A, Kolata, P, Cannone, G, Bellini, D, Barford, D and Allegretti, M (2024) Human spermatogenesis leads to a reduced nuclear pore structure and function. BioRxiv, 2024.10.30.620797. https://doi.org/10.1101/2024.10.30.620797CrossRefGoogle Scholar
Schaffer, M, Mahamid, J, Engel, BD, Laugks, T, Baumeister, W and Plitzko, JM (2017) Optimized cryo-focused ion beam sample preparation aimed at in situ structural studies of membrane proteins. Journal of Structural Biology 197(2), 7382. https://doi.org/10.1016/J.JSB.2016.07.010CrossRefGoogle ScholarPubMed
Schaffer, M, Pfeffer, S, Mahamid, J, Kleindiek, S, Laugks, T, Albert, S, Engel, BD, Rummel, A, Smith, AJ, Baumeister, W and Plitzko, JM (2019) A cryo-FIB lift-out technique enables molecular-resolution cryo-ET within native Caenorhabditis elegans tissue. Nature Methods 16(8), 757762. https://doi.org/10.1038/S41592-019-0497-5CrossRefGoogle ScholarPubMed
Scher, N, Rechav, K, Paul-Gilloteaux, P and Avinoam, O (2021) In situ fiducial markers for 3D correlative cryo-fluorescence and FIB-SEM imaging. IScience 24(7), 102714. https://doi.org/10.1016/j.isci.2021.102714CrossRefGoogle ScholarPubMed
Schertel, A, Snaidero, N, Han, HM, Ruhwedel, T, Laue, M, Grabenbauer, M and Möbius, W (2013) Cryo FIB-SEM: Volume imaging of cellular ultrastructure in native frozen specimens. Journal of Structural Biology 184(2), 355360. https://doi.org/10.1016/J.JSB.2013.09.024CrossRefGoogle ScholarPubMed
Schiøtz, OH, Kaiser, CJO, Klumpe, S, Morado, DR, Poege, M, Schneider, J, Beck, F, Klebl, DP, Thompson, C and Plitzko, JM (2023) Serial lift-out: Sampling the molecular anatomy of whole organisms. Nature Methods, 19. https://doi.org/10.1038/s41592-023-02113-5Google ScholarPubMed
Schur, FKM, Obr, M, Hagen, WJH, Wan, W, Jakobi, AJ, Kirkpatrick, JM, Sachse, C, Kräusslich, HG and Briggs, JAG (2016) An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation. Science 353(6298), 506508. https://doi.org/10.1126/SCIENCE.AAF9620CrossRefGoogle ScholarPubMed
Schwartz, O, Axelrod, JJ, Campbell, SL, Turnbaugh, C, Glaeser, RM and Müller, H (2019) Laser phase plate for transmission electron microscopy. Nature Methods 16(10), 10161020. https://doi.org/10.1038/s41592-019-0552-2CrossRefGoogle ScholarPubMed
Singh, D, Soni, N, Hutchings, J, Echeverria, I, Shaikh, F, Duquette, M, Suslov, S, Li, Z, van Eeuwen, T, Molloy, K, Shi, Y, Wang, J, Guo, Q, Chait, BT, Fernandez-Martinez, J, Rout, MP, Sali, A and Villa, E (2024) The molecular architecture of the nuclear basket. BioRxiv, 2024.03.27.587068. https://doi.org/10.1101/2024.03.27.587068CrossRefGoogle Scholar
Studer, D, Humbel, BM and Chiquet, M (2008) Electron microscopy of high pressure frozen samples: Bridging the gap between cellular ultrastructure and atomic resolution. Histochemistry and Cell Biology 130(5), 877889. https://doi.org/10.1007/S00418-008-0500-1CrossRefGoogle Scholar
Sviben, S, Gal, A, Hood, MA, Bertinetti, L, Politi, Y, Bennet, M, Krishnamoorthy, P, Schertel, A, Wirth, R, Sorrentino, A, Pereiro, E, Faivre, D and Scheffel, A (2016) A vacuole-like compartment concentrates a disordered calcium phase in a key coccolithophorid alga. Nature Communications 7(1), 19. https://doi.org/10.1038/ncomms11228CrossRefGoogle Scholar
Tacke, S, Erdmann, P, Wang, Z, Klumpe, S, Grange, M, Plitzko, J and Raunser, S (2021) A streamlined workflow for automated cryo focused ion beam milling. Journal of Structural Biology 213(3), 107743. https://doi.org/10.1016/J.JSB.2021.107743CrossRefGoogle ScholarPubMed
Tegunov, D, Xue, L, Dienemann, C, Cramer, P and Mahamid, J (2021) Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells. Nature Methods 18(2), 186193. https://doi.org/10.1038/s41592-020-01054-7CrossRefGoogle Scholar
Tamborrini, D, Wang, Z, Wagner, T, Tacke, S, Stabrin, M, Grange, M, Lin Kho, A, Rees, M, Bennett, P, Gautel, M, Raunser, S. Structure of the native myosin filament in the relaxed cardiac sarcomere. Nature 623, 863871 (2023). https://doi.org/10.1038/s41586-023-06690-5CrossRefGoogle ScholarPubMed
Tuijtel, MW, Cruz-León, S, Kreysing, JP, Welsch, S, Hummer, G, Beck, M and Turoňová, B (2024) Thinner is not always better: Optimizing cryo-lamellae for subtomogram averaging. Science Advances 10(17) https://doi.org/10.1126/SCIADV.ADK6285CrossRefGoogle Scholar
Turoňová, B, Sikora, M, Schürmann, C, Hagen, WJH, Welsch, S, Blanc, FEC, von Bülow, S, Gecht, M, Bagola, K, Hörner, C, van Zandbergen, G, Landry, J, de Azevedo, NTD, Mosalaganti, S, Schwarz, A, Covino, R, Mühlebach, MD, Hummer, G, Locker, JK and Beck, M (2020) In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges. Science 370(6513), 203208. https://doi.org/10.1126/SCIENCE.ABD5223CrossRefGoogle ScholarPubMed
Uchida, M, McDermott, G, Wetzler, M, Le Gros, MA, Myllys, M, Knoechel, C, Barron, AE and Larabell, CA (2009) Soft X-ray tomography of phenotypic switching and the cellular response to antifungal peptoids in Candida albicans. Proceedings of the National Academy of Sciences of the United States of America 106(46), 19375. https://doi.org/10.1073/PNAS.0906145106CrossRefGoogle ScholarPubMed
Vidavsky, N, Akiva, A, Kaplan-Ashiri, I, Rechav, K, Addadi, L, Weiner, S and Schertel, A (2016) Cryo-FIB-SEM serial milling and block face imaging: Large volume structural analysis of biological tissues preserved close to their native state. Journal of Structural Biology 196(3), 487495. https://doi.org/10.1016/J.JSB.2016.09.016CrossRefGoogle ScholarPubMed
Vidavsky, N, Masic, A, Schertel, A, Weiner, S and Addadi, L (2015) Mineral-bearing vesicle transport in sea urchin embryos. Journal of Structural Biology 192(3), 358365. https://doi.org/10.1016/J.JSB.2015.09.017CrossRefGoogle ScholarPubMed
Villa, E, Schaffer, M, Plitzko, JM and Baumeister, W (2013) Opening windows into the cell: Focused-ion-beam milling for cryo-electron tomography. Current Opinion in Structural Biology 23(5), 771777. https://doi.org/10.1016/J.SBI.2013.08.006CrossRefGoogle ScholarPubMed
von Kügelgen, A, Cassidy, CK, Van Dorst, S, Pagani, LL, Batters, C, Ford, Z, Löwe, J, Alva, V, Stansfeld, PJ and Tanmay Bharat, AM (2024) Membraneless channels sieve cations in ammonia-oxidizing marine archaea. Nature, 17. https://doi.org/10.1038/s41586-024-07462-5Google ScholarPubMed
von Kügelgen, A, Tang, H, Hardy, GG, Kureisaite-Ciziene, D, Brun, YV, Stansfeld, PJ, Robinson, CV and Bharat, TAM (2020) In situ structure of an intact lipopolysaccharide-bound bacterial surface layer. Cell 180(2), 348. https://doi.org/10.1016/J.CELL.2019.12.006CrossRefGoogle ScholarPubMed
Wagner, FR, Watanabe, R, Schampers, R, Singh, D, Persoon, H, Schaffer, M, Fruhstorfer, P., Plitzko, J and Villa, E (2020) Preparing samples from whole cells using focused-ion-beam milling for cryo-electron tomography. Nature Protocols 15(6), 20412070. https://doi.org/10.1038/s41596-020-0320-xCrossRefGoogle ScholarPubMed
Wagner, J, Carvajal, AI, Bracher, A, Beck, F, Wan, W, Bohn, S, Körner, R, Baumeister, W, Fernandez-Busnadiego, R and Hartl, FU (2024) Visualizing chaperonin function in situ by cryo-electron tomography. Nature 633(8029), 459464. https://doi.org/10.1038/s41586-024-07843-wCrossRefGoogle ScholarPubMed
Wagner, T, Lusnig, L, Pospich, S, Stabrin, M, Schonfeld, F and Raunser, S (2020) Two particle-picking procedures for filamentous proteins: SPHIRE-crYOLO filament mode and SPHIRE-STRIPER. Acta Crystallographica Section D: Structural Biology 76(7), 613620. https://doi.org/10.1107/S2059798320007342CrossRefGoogle ScholarPubMed
Wagner, T, Merino, F, Stabrin, M, Moriya, T, Antoni, C, Apelbaum, A, Hagel, P, Sitsel, O, Raisch, T, Prumbaum, D, Quentin, D, Roderer, D, Tacke, S, Siebolds, B, Schubert, E, Shaikh, TR, Lill, P, Gatsogiannis, C and Raunser, S (2019) SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Communications Biology 2(1), 113. https://doi.org/10.1038/s42003-019-0437-zCrossRefGoogle ScholarPubMed
Waltz, F, Righetto, RD, Kelley, R, Zhang, X, Obr, M, Khavnekar, S, Kotecha, A and Engel, BD (2024) In-cell architecture of the mitochondrial respiratory chain. BioRxiv, 2024.09.03.610704. https://doi.org/10.1101/2024.09.03.610704CrossRefGoogle Scholar
Wan, W, Khavnekar, S and Wagner, J (2024) STOPGAP: An open-source package for template matching, subtomogram alignment and classification. Acta Crystallographica Section D Structural Biology 80(5), 336349. https://doi.org/10.1107/S205979832400295XCrossRefGoogle ScholarPubMed
Wang, S, Zhou, H, Chen, W, Jiang, Y, Yan, X, You, H and Li, X (2023) CryoFIB milling large tissue samples for cryo-electron tomography. Scientific Reports 13(1), 112. https://doi.org/10.1038/s41598-023-32716-zGoogle ScholarPubMed
Wang, Z, Grange, M, Pospich, S, Wagner, T, Kho, AL, Gautel, M and Raunser, S (2022) Structures from intact myofibrils reveal mechanism of thin filament regulation through nebulin. Science 375(6582) https://doi.org/10.1126/science.abn1934CrossRefGoogle ScholarPubMed
Wang, Z, Grange, M, Wagner, T, Kho, AL, Gautel, M and Raunser, S (2021) The molecular basis for sarcomere organization in vertebrate skeletal muscle. Cell 184(8), 2135. https://doi.org/10.1016/J.CELL.2021.02.047CrossRefGoogle ScholarPubMed
Watanabe, R, Buschauer, R, Böhning, J, Audagnotto, M, Lasker, K, Lu, TW, Boassa, D, Taylor, S and Villa, E (2020) The in situ structure of Parkinson’s disease-linked LRRK2. Cell 182(6), 15081518.e16. https://doi.org/10.1016/J.CELL.2020.08.004CrossRefGoogle ScholarPubMed
Watanabe, R, Zyla, D, Parekh, D, Hong, C, Jones, Y, Schendel, SL, Wan, W, Castillon, G and Saphire, EO (2024) Intracellular Ebola virus nucleocapsid assembly revealed by in situ cryo-electron tomography. Cell 187(20), 55875603.e19. https://doi.org/10.1016/J.CELL.2024.08.044CrossRefGoogle ScholarPubMed
Weil, MT, Ruhwedel, T, Meschkat, M, Sadowski, B and Möbius, W (2019) Transmission electron microscopy of oligodendrocytes and myelin. Methods in Molecular Biology 1936, 343375. https://doi.org/10.1007/978-1-4939-9072-6_20CrossRefGoogle ScholarPubMed
Weiner, A, Kapishnikov, S, Shimoni, E, Cordes, S, Guttmann, P, Schneider, G and Elbaum, M (2013) Vitrification of thick samples for soft X-ray cryo-tomography by high pressure freezing. Journal of Structural Biology 181(1), 7781. https://doi.org/10.1016/J.JSB.2012.10.005CrossRefGoogle ScholarPubMed
Weiß, D, Schneider, G, Niemann, B, Guttmann, P, Rudolph, D and Schmahl, G (2000) Computed tomography of cryogenic biological specimens based on X-ray microscopic images. Ultramicroscopy 84(3–4), 185197. https://doi.org/10.1016/S0304-3991(00)00034-6CrossRefGoogle ScholarPubMed
Wieferig, JP, Mills, DJ and Kühlbrandt, W (2021) Devitrification reduces beam-induced movement in cryo-EM. IUCrJ 8(2), 186194. https://doi.org/10.1107/S2052252520016243CrossRefGoogle ScholarPubMed
Wolf, SG and Elbaum, M (2019) CryoSTEM tomography in biology. Methods in Cell Biology 152, 197215. https://doi.org/10.1016/BS.MCB.2019.04.001CrossRefGoogle ScholarPubMed
Wolf, SG, Houben, L and Elbaum, M (2014) Cryo-scanning transmission electron tomography of vitrified cells. Nature Methods 11(4), 423428. https://doi.org/10.1038/nmeth.2842CrossRefGoogle ScholarPubMed
Wolf, SG, Mutsafi, Y, Dadosh, T, Ilani, T, Lansky, Z, Horowitz, B, Rubin, S, Elbaum, M and Fass, D (2017) 3D visualization of mitochondrial solid-phase calcium stores in whole cells. ELife 6. https://doi.org/10.7554/ELIFE.29929CrossRefGoogle ScholarPubMed
Wozny, MR, Di Luca, A, Morado, DR, Picco, A, Khaddaj, R, Campomanes, P, Ivanović, L, Hoffmann, PC, Miller, EA, Vanni, S and Kukulski, W (2023) In situ architecture of the ER–mitochondria encounter structure. Nature 618(7963), 188192. https://doi.org/10.1038/s41586-023-06050-3CrossRefGoogle ScholarPubMed
Xu, CS, Hayworth, KJ, Lu, Z, Grob, P, Hassan, AM, García-Cerdán, JG, Niyogi, KK, Nogales, E, Weinberg, RJ and Hess, HF (2017) Enhanced FIB-SEM systems for large-volume 3D imaging. ELife 6. https://doi.org/10.7554/ELIFE.25916CrossRefGoogle ScholarPubMed
Xu, CS, Pang, S, Shtengel, G, Müller, A, Ritter, AT, Hoffman, HK, ya Takemura, S, Lu, Z, Pasolli, HA, Iyer, N, Chung, J, Bennett, D, Weigel, AV, Freeman, M, van Engelenburg, SB, Walther, TC, Farese, RV, Lippincott-Schwartz, J, Mellman, I, … Hess, HF (2021) An open-access volume electron microscopy atlas of whole cells and tissues. Nature 599(7883), 147151. https://doi.org/10.1038/s41586-021-03992-4CrossRefGoogle ScholarPubMed
Xue, L, Lenz, S, Zimmermann-Kogadeeva, M, Tegunov, D, Cramer, P, Bork, P, Rappsilber, J and Mahamid, J (2022) Visualizing translation dynamics at atomic detail inside a bacterial cell. Nature 610(7930), 205211. https://doi.org/10.1038/s41586-022-05255-2CrossRefGoogle ScholarPubMed
Yang, JE, Larson, MR, Sibert, BS, Kim, JY, Parrell, D, Sanchez, JC, Pappas, V, Kumar, A, Cai, K, Thompson, K and Wright, ER (2023) Correlative montage parallel array cryo-tomography for in situ structural cell biology. Nature Methods 20(10), 15371543. https://doi.org/10.1038/s41592-023-01999-5CrossRefGoogle ScholarPubMed
Yang, J, Vrbovská, V, Franke, T, Sibert, B, Larson, M, Coomes, T, Rigort, A, Mitchels, J and Wright, E R. (2023) Precise 3D localization by integrated fluorescence microscopy (iFLM) for cryo-FIB-milling and in-situ cryo-ET. Microscopy and Microanalysis (Supplement_1), 10551057. https://doi.org/10.1093/MICMIC/OZAD067.541CrossRefGoogle Scholar
You, X, Zhang, X, Cheng, J, Xiao, Y, Ma, J, Sun, S, Zhang, X, Wang, HW and Sui, SF (2023) In situ structure of the red algal phycobilisome–PSII–PSI–LHC megacomplex. Nature 616(7955), 199206. https://doi.org/10.1038/s41586-023-05831-0CrossRefGoogle ScholarPubMed
Zachs, T, Schertel, A, Medeiros, J, Weiss, GL, Hugener, J, Matos, J and Pilhofer, M (2020) Fully automated, sequential focused ion beam milling for cryo-electron tomography. ELife 9. https://doi.org/10.7554/ELIFE.52286CrossRefGoogle ScholarPubMed
Zens, B, Fäßler, F, Hansen, JM, Hauschild, R, Datler, J, Hodirnau, V-V, Zheden, V, Alanko, J, Sixt, M and Schur, FKM (2024) Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology 223(6) https://doi.org/10.1083/JCB.202309125CrossRefGoogle ScholarPubMed
Zhang, J, Zhang, D, Sun, L, Ji, G, Huang, X, Niu, T, Xu, J, Ma, C, Zhu, Y, Gao, N, Xu, W and Sun, F (2021) VHUT-cryo-FIB, a method to fabricate frozen hydrated lamellae from tissue specimens for in situ cryo-electron tomography. Journal of Structural Biology 213(3), 107763. https://doi.org/10.1016/J.JSB.2021.107763CrossRefGoogle ScholarPubMed
Zhang, P (2019) Advances in cryo-electron tomography and subtomogram averaging and classification. Current Opinion in Structural Biology, 58 249258. https://doi.org/10.1016/J.SBI.2019.05.021CrossRefGoogle ScholarPubMed
Zhang, X, Sridharan, S, Zagoriy, I, Eugster Oegema, C, Ching, C, Pflaesterer, T, Fung, HKH, Becher, I, Poser, I, Müller, CW, Hyman, AA, Savitski, MM and Mahamid, J (2023) Molecular mechanisms of stress-induced reactivation in mumps virus condensates. Cell 186(9), 18771894.e27. https://doi.org/10.1016/J.CELL.2023.03.015CrossRefGoogle ScholarPubMed
Zheng, S, Wolff, G, Greenan, G, Chen, Z, Faas, FGA, Bárcena, M, Koster, AJ, Cheng, Y and Agard, DA (2022) AreTomo: An integrated software package for automated marker-free, motion-corrected cryo-electron tomographic alignment and reconstruction. Journal of Structural Biology: X 6, 100068. https://doi.org/10.1016/J.YJSBX.2022.100068Google ScholarPubMed
Zhong, X, Wade, CA, Withers, PJ, Zhou, X, Cai, C, Haigh, SJ and Burke, MG (2021) Comparing Xe+pFIB and Ga+FIB for TEM sample preparation of Al alloys: Minimising FIB-induced artefacts. Journal of Microscopy 282(2), 101. https://doi.org/10.1111/JMI.12983CrossRefGoogle ScholarPubMed
Zimmerli, CE, Allegretti, M, Rantos, V, Goetz, SK, Obarska-Kosinska, A, Zagoriy, I, Halavatyi, A, Hummer, G, Mahamid, J, Kosinski, J and Beck, M (2021) Nuclear pores dilate and constrict in cellulo. Science 374(6573) https://doi.org/10.1126/science.abd9776CrossRefGoogle ScholarPubMed
Zivanov, J, Otón, J, Ke, Z, von Kügelgen, A, Pyle, E, Qu, K, Morado, D, Castaño-Díez, D, Zanetti, G, Bharat, TA, Briggs, JA and Scheres, SH (2022) A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0. ELife 11. https://doi.org/10.7554/ELIFE.83724CrossRefGoogle Scholar