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Bridging structural and cell biology with cryo-electron microscopy

Abstract

Most life scientists would agree that understanding how cellular processes work requires structural knowledge about the macromolecules involved. For example, deciphering the double-helical nature of DNA revealed essential aspects of how genetic information is stored, copied and repaired. Yet, being reductionist in nature, structural biology requires the purification of large amounts of macromolecules, often trimmed off larger functional units. The advent of cryogenic electron microscopy (cryo-EM) greatly facilitated the study of large, functional complexes and generally of samples that are hard to express, purify and/or crystallize. Nevertheless, cryo-EM still requires purification and thus visualization outside of the natural context in which macromolecules operate and coexist. Conversely, cell biologists have been imaging cells using a number of fast-evolving techniques that keep expanding their spatial and temporal reach, but always far from the resolution at which chemistry can be understood. Thus, structural and cell biology provide complementary, yet unconnected visions of the inner workings of cells. Here we discuss how the interplay between cryo-EM and cryo-electron tomography, as a connecting bridge to visualize macromolecules in situ, holds great promise to create comprehensive structural depictions of macromolecules as they interact in complex mixtures or, ultimately, inside the cell itself.

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Fig. 1: A structural biologist’s dream.
Fig. 2: Characterizing Increasing sample complexity by a continuum of cryo-EM methods.
Fig. 3: Cryo-ET visualizes complex cell biology.
Fig. 4: In situ cryo-EM with 2D template matching.

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References

  1. Berman, H., Henrick, K. & Nakamura, H. Announcing the worldwide Protein Data Bank. Nat. Struct. Biol. 10, 980 (2003).

    CAS  PubMed  Google Scholar 

  2. Robinson, C. V., Sali, A. & Baumeister, W. The molecular sociology of the cell. Nature 450, 973–982 (2007). This seminal review coined the termmolecular sociologyand set the scene for future in situ structural biology that combines cryo-ET with proteomics via integrative modelling.

    ADS  CAS  PubMed  Google Scholar 

  3. Span, E. A. et al. Protein structure in context: the molecular landscape of angiogenesis. Biochem. Mol. Biol. Educ. 41, 213–223 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Bäuerlein, F. J. B. & Baumeister, W. Towards visual proteomics at high resolution. J. Mol. Biol. 433, 167187 (2021).

    PubMed  Google Scholar 

  5. Berger, C. et al. Cryo-electron tomography on focused ion beam lamellae transforms structural cell biology. Nat. Methods 20, 499–511 (2023).

    CAS  PubMed  Google Scholar 

  6. Chua, E. Y. D. et al. Better, faster, cheaper: recent advances in cryo-electron microscopy. Annu. Rev. Biochem. 91, 1–32 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Wu, M. & Lander, G. C. Present and emerging methodologies in cryo-EM single-particle analysis. Biophys. J. 119, 1281–1289 (2020).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  8. Young, L. N. & Villa, E. Bringing structure to cell biology with cryo-electron tomography. Annu. Rev. Biophys. 52, 573–595 (2023).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Kühlbrandt, W. The resolution revolution. Science 343, 1443–1444 (2014).

    ADS  PubMed  Google Scholar 

  10. Lewis, J. S. et al. Mechanism of replication origin melting nucleated by CMG helicase assembly. Nature 606, 1007–1014 (2022).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  11. Chen, S. et al. Structural basis of long-range to short-range synaptic transition in NHEJ. Nature 593, 294–298 (2021).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  12. Chen, X. et al. Structures of +1 nucleosome-bound PIC–Mediator complex. Science 378, 62–68 (2022). This study is an inspiring example of the large size and complexity of reconstitution systems amenable for cryo-EM study. It visualized an assembly of eight transcription complexes, some over 1 MDa in size, on chromatin.

    ADS  CAS  PubMed  Google Scholar 

  13. Tholen, J., Razew, M., Weis, F. & Galej, W. P. Structural basis of branch site recognition by the human spliceosome. Science 375, 50–57 (2022).

    ADS  CAS  PubMed  Google Scholar 

  14. Fromm, S. A. et al. The translating bacterial ribosome at 1.55 Å resolution generated by cryo-EM imaging services. Nat. Commun. 14, 1095 (2023).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  15. Gestaut, D. et al. Structural visualization of the tubulin folding pathway directed by human chaperonin TRiC/CCT. Cell 185, 4770–4787.e20 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Bashore, C. et al. Targeted degradation via direct 26S proteasome recruitment. Nat. Chem. Biol. 19, 55–63 (2023).

    CAS  PubMed  Google Scholar 

  17. Zhang, K., Julius, D. & Cheng, Y. Structural snapshots of TRPV1 reveal mechanism of polymodal functionality. Cell 184, 5138–5150.e12 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Kern, D. M. et al. Cryo-EM structure of SARS-CoV-2 ORF3a in lipid nanodiscs. Nat. Struct. Mol. Biol. 28, 573–582 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Lin, X. et al. Cryo-EM structures of orphan GPR21 signaling complexes. Nat. Commun. 14, 216 (2023).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  20. Domínguez-Martín, M. A. et al. Structures of a phycobilisome in light-harvesting and photoprotected states. Nature 609, 835–845 (2022).

    ADS  PubMed  Google Scholar 

  21. Oosterheert, W., Klink, B. U., Belyy, A., Pospich, S. & Raunser, S. Structural basis of actin filament assembly and aging. Nature 611, 374–379 (2022).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  22. Reynolds, M. J., Hachicho, C., Carl, A. G., Gong, R. & Alushin, G. M. Bending forces and nucleotide state jointly regulate F-actin structure. Nature 611, 380–386 (2022).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  23. Nakane, T. et al. Single-particle cryo-EM at atomic resolution. Nature 587, 152–156 (2020).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  24. Beck, M. & Baumeister, W. Cryo-electron tomography: can it reveal the molecular sociology of cells in atomic detail? Trends Cell Biol. 26, 825–837 (2016). A landmark review that discusses how recent technological breakthroughs in sample thinning, combined with direct electron detection and phase plates, hold promise to achieve near-atomic reconstructions by in situ cryo-ET.

    PubMed  Google Scholar 

  25. Al-Amoudi, A., Studer, D. & Dubochet, J. Cutting artefacts and cutting process in vitreous sections for cryo-electron microscopy. J. Struct. Biol. 150, 109–121 (2005).

    CAS  PubMed  Google Scholar 

  26. McDowall, A. W. et al. Electron microscopy of frozen hydrated sections of vitreous ice and vitrified biological samples. J. Microsc. 131, 1–9 (1983).

    CAS  PubMed  Google Scholar 

  27. Gan, L., Ng, C. T., Chen, C. & Cai, S. A collection of yeast cellular electron cryotomography data. Gigascience 8, giz077 (2019).

    PubMed  PubMed Central  Google Scholar 

  28. Marko, M., Hsieh, C., Schalek, R., Frank, J. & Mannella, C. Focused-ion-beam thinning of frozen-hydrated biological specimens for cryo-electron microscopy. Nat. Methods 4, 215–217 (2007).

    CAS  PubMed  Google Scholar 

  29. Rigort, A. et al. Focused ion beam micromachining of eukaryotic cells for cryoelectron tomography. Proc. Natl Acad. Sci. USA 109, 4449–4454 (2012).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  30. Schaffer, M. et al. Optimized cryo-focused ion beam sample preparation aimed at in situ structural studies of membrane proteins. J. Struct. Biol. 197, 73–82 (2017).

    CAS  PubMed  Google Scholar 

  31. Wagner, F. R. et al. Preparing samples from whole cells using focused-ion-beam milling for cryo-electron tomography. Nat. Protoc. 15, 2041–2070 (2020).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Lucic, V., Rigort, A. & Baumeister, W. Cryo-electron tomography: the challenge of doing structural biology in situ. J. Cell Biol. 202, 407–419 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Faruqi, A. R. & McMullan, G. Direct imaging detectors for electron microscopy. Nucl. Instrum. Methods Phys. Res. Sect. A 878, 180–190 (2018).

    ADS  CAS  Google Scholar 

  34. Campbell, M. G. et al. Movies of ice-embedded particles enhance resolution in electron cryo-microscopy. Structure 20, 1823–1828 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Schaffer, M. et al. A cryo-FIB lift-out technique enables molecular-resolution cryo-ET within native Caenorhabditis elegans tissue. Nat. Methods 16, 757–762 (2019).

    CAS  PubMed  Google Scholar 

  36. Kelley, K. et al. Waffle method: a general and flexible approach for improving throughput in FIB-milling. Nat. Commun. 13, 1857 (2022).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  37. Schiøtz, O. H. et al. Serial lift-out: sampling the molecular anatomy of whole organisms. Nat. Methods https://doi.org/10.1038/s41592-023-02113-5 (2023). This work presents developments that substantially improve success rates and reproducibility in cryo-FIB micromachining and micromanipulator-assisted lift-out for production of samples suitable for cryo-ET from small multicellular model organisms.

    Article  PubMed  Google Scholar 

  38. Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).

    CAS  PubMed  Google Scholar 

  39. Scheres, S. H. W. Processing of structurally heterogeneous cryo-EM data in RELION. Methods Enzymol. 579, 125–157 (2016).

    CAS  PubMed  Google Scholar 

  40. Zhong, E. D., Bepler, T., Berger, B. & Davis, J. H. CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks. Nat. Methods 18, 176–185 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Tegunov, D., Xue, L., Dienemann, C., Cramer, P. & Mahamid, J. Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells. Nat. Methods 18, 186–193 (2021). This work developed algorithms that allowed correction of sample deformation during cryo-ET acquisition to obtain, to our knowledge, the first near-atomic reconstruction of a macromolecular complex inside cells.

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Wan, W., Khavnekar, S., Wagner, J., Erdmann, P. & Baumeister, W. STOPGAP: a software package for subtomogram averaging and refinement. Microsc. Microanal. 26, 2516 (2020).

    ADS  Google Scholar 

  43. Zivanov, J. et al. A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0. eLife 11, e83724 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Powell, B. M. & Davis, J. H. Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN. Preprint at bioRxiv https://doi.org/10.1101/2023.05.31.542975 (2023).

  45. Rangan, R. et al. Deep reconstructing generative networks for visualizing dynamic biomolecules inside cells. Preprint at bioRxiv https://doi.org/10.1101/2023.08.18.553799 (2023).

  46. Allard, C. A. H. et al. Structural basis of sensory receptor evolution in octopus. Nature 616, 373–377 (2023).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  47. Xu, W. et al. Structural basis for strychnine activation of human bitter taste receptor TAS2R46. Science 377, 1298–1304 (2022).

    ADS  CAS  PubMed  Google Scholar 

  48. Yao, X., Fan, X. & Yan, N. Cryo-EM analysis of a membrane protein embedded in the liposome. Proc. Natl Acad. Sci. USA 117, 18497–18503 (2020).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  49. Mühleip, A. et al. Structural basis of mitochondrial membrane bending by the I–II–III2–IV2 supercomplex. Nature 615, 934–938 (2023).

    ADS  PubMed  PubMed Central  Google Scholar 

  50. Vallese, F. et al. Architecture of the human erythrocyte ankyrin-1 complex. Nat. Struct. Mol. Biol. 29, 706–718 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Walton, T. et al. Axonemal structures reveal mechanoregulatory and disease mechanisms. Nature https://doi.org/10.1038/s41586-023-06140-2 (2023).

  52. Abdella, R. et al. Structure of the human Mediator-bound transcription preinitiation complex. Science 372, 52–56 (2021).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  53. Herbst, D. A. et al. Structure of the human SAGA coactivator complex. Nat. Struct. Mol. Biol. 28, 989–996 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Liu, H., Li, A., Rochaix, J.-D. & Liu, Z. Architecture of chloroplast TOC–TIC translocon supercomplex. Nature 615, 349–357 (2023).

    ADS  CAS  PubMed  Google Scholar 

  55. Kelly, D. F., Abeyrathne, P. D., Dukovski, D. & Walz, T. The affinity grid: a pre-fabricated EM grid for monolayer purification. J. Mol. Biol. 382, 423–433 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Han, B.-G. et al. Long shelf-life streptavidin support-films suitable for electron microscopy of biological macromolecules. J. Struct. Biol. 195, 238–244 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  57. Wang, F. et al. General and robust covalently linked graphene oxide affinity grids for high-resolution cryo-EM. Proc. Natl Acad. Sci. USA 117, 24269–24273 (2020).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  58. Maldonado, M., Guo, F. & Letts, J. A. Atomic structures of respiratory complex III2, complex IV, and supercomplex III2–IV from vascular plants. eLife 10, e62047 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Peukes, J. et al. The native structure of the assembled matrix protein 1 of influenza A virus. Nature 587, 495–498 (2020).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  60. Pacheco-Fiallos, B. et al. mRNA recognition and packaging by the human transcription–export complex. Nature 616, 828–835 (2023). This study is an example of the combination of single-particle cryo-EM and cryo-ET in the structural characterization of a complex biological assembly.

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  61. Ferro, L. S. et al. Structural and functional insight into regulation of kinesin-1 by microtubule-associated protein MAP7. Science 375, 326–331 (2022).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  62. Hooy, R. M., Iwamoto, Y., Tudorica, D. A., Ren, X. & Hurley, J. H. Self-assembly and structure of a clathrin-independent AP-1:Arf1 tubular membrane coat. Sci. Adv. 8, eadd3914 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Verbeke, E. J., Mallam, A. L., Drew, K., Marcotte, E. M. & Taylor, D. W. Classification of single particles from human cell extract reveals distinct structures. Cell Rep. 24, 259–268.e3 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  64. Kastritis, P. L. et al. Capturing protein communities by structural proteomics in a thermophilic eukaryote. Mol. Syst. Biol. 13, 936 (2017).

    PubMed  PubMed Central  Google Scholar 

  65. Ho, C.-M. et al. Native structure of the RhopH complex, a key determinant of malaria parasite nutrient acquisition. Proc. Natl Acad. Sci. USA 118, e2100514118 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  66. Su, C.-C. et al. A ‘build and retrieve’ methodology to simultaneously solve cryo-EM structures of membrane proteins. Nat. Methods 18, 69–75 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  67. Danev, R. & Baumeister, W. Expanding the boundaries of cryo-EM with phase plates. Curr. Opin. Struct. Biol. 46, 87–94 (2017).

    CAS  PubMed  Google Scholar 

  68. Schwartz, O. et al. Laser phase plate for transmission electron microscopy. Nat. Methods 16, 1016–1020 (2019). This study represents an exciting hardware development with impacts in the applicability and interpretability of both cryo-EM and cryo-ET by dramatically improving the contrast of the images and eliminating the requirement for large defocus.

    CAS  PubMed  PubMed Central  Google Scholar 

  69. Jijumon, A. S. et al. Lysate-based pipeline to characterize microtubule-associated proteins uncovers unique microtubule behaviours. Nat. Cell Biol. 24, 253–267 (2022).

    CAS  PubMed  Google Scholar 

  70. Yi, X., Verbeke, E. J., Chang, Y., Dickinson, D. J. & Taylor, D. W. Electron microscopy snapshots of single particles from single cells. J. Biol. Chem. 294, 1602–1608 (2019).

    CAS  PubMed  Google Scholar 

  71. Studer, D., Graber, W., Al-Amoudi, A. & Eggli, P. A new approach for cryofixation by high-pressure freezing. J. Microsc. 203, 285–294 (2001).

    MathSciNet  CAS  PubMed  Google Scholar 

  72. Kuba, J. et al. Advanced cryo-tomography workflow developments—correlative microscopy, milling automation and cryo-lift-out. J. Microsc. 281, 112–124 (2021).

    CAS  PubMed  Google Scholar 

  73. Engel, L. et al. Lattice micropatterning for cryo-electron tomography studies of cell–cell contacts. J. Struct. Biol. 213, 107791 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  74. Toro-Nahuelpan, M. et al. Tailoring cryo-electron microscopy grids by photo-micropatterning for in-cell structural studies. Nat. Methods 17, 50–54 (2020).

    CAS  PubMed  Google Scholar 

  75. Gorelick, S. et al. PIE-scope, integrated cryo-correlative light and FIB/SEM microscopy. eLife 8, e45919 (2019).

    PubMed  PubMed Central  Google Scholar 

  76. Boltje, D. B. et al. A cryogenic, coincident fluorescence, electron, and ion beam microscope. eLife 11, e82891 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  77. Smeets, M. et al. Correlative cryo-FIB milling using METEOR, an integrated fluorescent light microscope. Microsc. Microanal. 28, 1310–1310 (2022).

    ADS  Google Scholar 

  78. Li, W. et al. Integrated multimodality microscope for accurate and efficient target-guided cryo-lamellae preparation. Nat. Methods 20, 268–275 (2023).

    CAS  PubMed  PubMed Central  Google Scholar 

  79. Klumpe, S. et al. A modular platform for automated cryo-FIB workflows. eLife 10, e70506 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  80. Dutka, M. & Prokhodtseva, A. AutoTEM 5—fully automated TEM sample preparation for materials science. Microsc. Microanal. 25, 554–555 (2019).

    ADS  Google Scholar 

  81. Eisenstein, F., Danev, R. & Pilhofer, M. Improved applicability and robustness of fast cryo-electron tomography data acquisition. J. Struct. Biol. 208, 107–114 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  82. Eisenstein, F. et al. Parallel cryo electron tomography on in situ lamellae. Nat. Methods 20, 131–138 (2023).

    CAS  PubMed  Google Scholar 

  83. Khavnekar, S. et al. Multishot tomography for high-resolution in situ subtomogram averaging. J. Struct. Biol. 215, 107911 (2023).

    CAS  PubMed  Google Scholar 

  84. Krull, A., Buchholz, T.-O. & Jug, F. Noise2Void—learning denoising from single noisy images. In IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) https://doi.org/10.1109/CVPR.2019.00223 (2019).

  85. Lehtinen, J. et al. Noise2Noise: learning image restoration without clean data. In Proc. 35th Intl Conf. Machine Learning, PMLR 80, 2965–2974 (2018).

  86. Liu, Y.-T. et al. Isotropic reconstruction for electron tomography with deep learning. Nat. Commun. 13, 6482 (2022).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  87. Böhm, J. et al. Toward detecting and identifying macromolecules in a cellular context: template matching applied to electron tomograms. Proc. Natl Acad. Sci. USA 97, 14245–14250 (2000). This study developed the computational method, tested in “phantom” cells, that allows localization of macromolecular complexes with known structures in cryo-ET data.

    ADS  PubMed  PubMed Central  Google Scholar 

  88. de Teresa-Trueba, I. et al. Convolutional networks for supervised mining of molecular patterns within cellular context. Nat. Methods 20, 284–294 (2023).

    PubMed  PubMed Central  Google Scholar 

  89. Moebel, E. et al. Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms. Nat. Methods 18, 1386–1394 (2021).

    CAS  PubMed  Google Scholar 

  90. Rice, G. et al. TomoTwin: generalized 3D localization of macromolecules in cryo-electron tomograms with structural data mining. Nat. Methods 20, 871–880 (2023).

    CAS  PubMed  PubMed Central  Google Scholar 

  91. Arnold, J. et al. Site-specific cryo-focused ion beam sample preparation guided by 3D correlative microscopy. Biophys. J. 110, 860–869 (2016).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  92. Ganeva, I. & Kukulski, W. Membrane architecture in the spotlight of correlative microscopy. Trends Cell Biol. 30, 577–587 (2020).

    CAS  PubMed  Google Scholar 

  93. Kukulski, W. et al. Correlated fluorescence and 3D electron microscopy with high sensitivity and spatial precision. J. Cell Biol. 192, 111–119 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  94. Sartori, A. et al. Correlative microscopy: bridging the gap between fluorescence light microscopy and cryo-electron tomography. J. Struct. Biol. 160, 135–145 (2007).

    PubMed  Google Scholar 

  95. Dahlberg, P. D. & Moerner, W. E. Cryogenic super-resolution fluorescence and electron microscopy correlated at the nanoscale. Annu. Rev. Phys. Chem. 72, 253–278 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  96. Dahlberg, P. D. et al. Cryogenic single-molecule fluorescence annotations for electron tomography reveal in situ organization of key proteins in Caulobacter. Proc. Natl Acad. Sci. USA 117, 13937–13944 (2020).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  97. Tuijtel, M. W., Koster, A. J., Jakobs, S., Faas, F. G. A. & Sharp, T. H. Correlative cryo super-resolution light and electron microscopy on mammalian cells using fluorescent proteins. Sci. Rep. 9, 1369 (2019).

    ADS  PubMed  PubMed Central  Google Scholar 

  98. Wang, Q., Mercogliano, C. P. & Löwe, J. A ferritin-based label for cellular electron cryotomography. Structure 19, 147–154 (2011).

    CAS  PubMed  Google Scholar 

  99. Silvester, E. et al. DNA origami signposts for identifying proteins on cell membranes by electron cryotomography. Cell 184, 1110–1121.e16 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  100. Fung, H. K. H. et al. Genetically encoded multimeric tags for subcellular protein localization in cryo-EM. Nat. Methods 20, 1900–1908 (2023).

    CAS  PubMed  PubMed Central  Google Scholar 

  101. Schorb, M., Haberbosch, I., Hagen, W. J. H., Schwab, Y. & Mastronarde, D. N. Software tools for automated transmission electron microscopy. Nat. Methods 16, 471–477 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  102. Lucas, B. A. & Grigorieff, N. Quantification of gallium cryo-FIB milling damage in biological lamellae. Proc. Natl Acad. Sci. USA 120, e2301852120 (2023).

    CAS  PubMed  PubMed Central  Google Scholar 

  103. Berger, C. et al. Plasma FIB milling for the determination of structures in situ. Nat. Commun. 14, 629 (2023).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  104. Laughlin, T. G. et al. Architecture and self-assembly of the jumbo bacteriophage nuclear shell. Nature 608, 429–435 (2022).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  105. Lacey, S. E., Foster, H. E. & Pigino, G. The molecular structure of IFT-A and IFT-B in anterograde intraflagellar transport trains. Nat. Struct. Mol. Biol. 30, 584–593 (2023).

    CAS  PubMed  PubMed Central  Google Scholar 

  106. Wozny, M. R. et al. In situ architecture of the ER–mitochondria encounter structure. Nature https://doi.org/10.1038/s41586-023-06050-3 (2023).

  107. Baek, M. et al. Accurate prediction of protein structures and interactions using a three-track neural network. Science 373, 871–876 (2021).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  108. Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  109. Graziadei, A. & Rappsilber, J. Leveraging crosslinking mass spectrometry in structural and cell biology. Structure 30, 37–54 (2022).

    CAS  PubMed  Google Scholar 

  110. O’Reilly, F. J. et al. In-cell architecture of an actively transcribing-translating expressome. Science 369, 554–557 (2020). This study combines cellular cryo-ET with in-cell crosslinking and whole-cell proteomics, and illustrates the power of integrative approaches to capture elusive and transient complexes.

    ADS  PubMed  PubMed Central  Google Scholar 

  111. Lucas, B. A. et al. Locating macromolecular assemblies in cells by 2D template matching with cisTEM. eLife 10, e68946 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  112. Rickgauer, J. P., Grigorieff, N. & Denk, W. Single-protein detection in crowded molecular environments in cryo-EM images. eLife 6, e25648 (2017).

    PubMed  PubMed Central  Google Scholar 

  113. Lucas, B. A., Himes, B. A. & Grigorieff, N. Baited reconstruction with 2D template matching for high-resolution structure determination in vitro and in vivo without template bias. eLife 12, RP90486 (2023).

    PubMed  PubMed Central  Google Scholar 

  114. Narayan, K. & Subramaniam, S. Focused ion beams in biology. Nat. Methods 12, 1021–1031 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  115. Xu, C. S. et al. An open-access volume electron microscopy atlas of whole cells and tissues. Nature 599, 147–151 (2021).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  116. Smith, D. & Starborg, T. Serial block face scanning electron microscopy in cell biology: applications and technology. Tissue Cell 57, 111–122 (2019).

    PubMed  Google Scholar 

  117. Harkiolaki, M. et al. Cryo-soft X-ray tomography: using soft X-rays to explore the ultrastructure of whole cells. Emerg. Top. Life Sci. 2, 81–92 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  118. Mahamid, J. et al. Visualizing the molecular sociology at the HeLa cell nuclear periphery. Science 351, 969–972 (2016).

    ADS  CAS  PubMed  Google Scholar 

  119. Kasinath, V. et al. JARID2 and AEBP2 regulate PRC2 in the presence of H2AK119ub1 and other histone modifications. Science 371, eabc3393 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  120. Mosalaganti, S. et al. AI-based structure prediction empowers integrative structural analysis of human nuclear pores. Science 376, eabm9506 (2022). This study capitalizes on AlphaFold2 and cryo-ET data for structural modelling of the human nuclear pore complex with unprecedented precision and completeness.

    CAS  PubMed  Google Scholar 

  121. Gemmer, M. et al. Visualization of translation and protein biogenesis at the ER membrane. Nature 614, 160–167 (2023).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  122. Hoffmann, P. C. et al. Tricalbins contribute to cellular lipid flux and form curved ER–PM contacts that are bridged by rod-shaped structures. Dev. Cell 51, 488–502.e8 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  123. Lucas, B. A., Zhang, K., Loerch, S. & Grigorieff, N. In situ single particle classification reveals distinct 60S maturation intermediates in cells. eLife 11, e79272 (2022).

    CAS  PubMed  PubMed Central  Google Scholar 

  124. De Rosier, D. J. & Klug, A. Reconstruction of three dimensional structures from electron micrographs. Nature 217, 130–134 (1968).

    ADS  PubMed  Google Scholar 

  125. Dubochet, J. & McDowall, A. W. Vitrification of pure water for electron microscopy. J. Microsc. 124, RP3–RP4 (1981).

    Google Scholar 

  126. Frank, J. Averaging of low exposure electron micrographs of non-periodic objects. Ultramicroscopy 1, 159–162 (1975).

    CAS  PubMed  Google Scholar 

  127. Hart, R. G. Electron microscopy of unstained biological material: the polytropic montage. Science 159, 1464–1467 (1968).

    ADS  CAS  PubMed  Google Scholar 

  128. Cheng, Y., Grigorieff, N., Penczek, P. A. & Walz, T. A primer to single-particle cryo-electron microscopy. Cell 161, 438–449 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  129. Chen, Z. et al. In situ cryo-electron tomography reveals the asymmetric architecture of mammalian sperm axonemes. Nat. Struct. Mol. Biol. 30, 360–369 (2023).

    CAS  PubMed  PubMed Central  Google Scholar 

  130. Hoffmann, P. C. et al. Structures of the eukaryotic ribosome and its translational states in situ. Nat. Commun. 13, 7435 (2022).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  131. Wan, W. & Briggs, J. A. G. Cryo-electron tomography and subtomogram averaging. Methods Enzymol. 579, 329–367 (2016).

    CAS  PubMed  Google Scholar 

  132. Wang, Z. et al. The molecular basis for sarcomere organization in vertebrate skeletal muscle. Cell 184, 2135–2150.e13 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  133. Pyle, E. & Zanetti, G. Current data processing strategies for cryo-electron tomography and subtomogram averaging. Biochem. J. 478, 1827–1845 (2021).

    CAS  PubMed  Google Scholar 

  134. wwPDB Consortium. Protein Data Bank: the single global archive for 3D macromolecular structure data. Nucleic Acids Res. 47, D520–D528 (2018).

    Google Scholar 

  135. Lawson, C. L. et al. EMDataBank unified data resource for 3DEM. Nucleic Acids Res. 44, D396–D403 (2016).

    CAS  PubMed  Google Scholar 

  136. Iudin, A. et al. EMPIAR: the Electron Microscopy Public Image Archive. Nucleic Acids Res. 51, D1503–D1511 (2023).

    PubMed  Google Scholar 

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Acknowledgements

We are grateful to our group members and many colleagues for fruitful discussions. We thank those who provided figures for reproduction in this Review, and we apologize to those whose outstanding work we have not been able to cite due to the limited number of references. E.N. acknowledges support from the US National Institutes of Health (R35GM127018), the European Research Council (ERC-2022-SYG 101071583), and is a Howard Hughes Medical Institute Investigator. J.M. acknowledges valuable assistance from J. Dobbs, support from the EMBL, a European Research Council starting grant (3DCellPhase- 760067) and a Chan-Zuckerberg Initiative grant for Visual Proteomics.

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Correspondence to Eva Nogales or Julia Mahamid.

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Nogales, E., Mahamid, J. Bridging structural and cell biology with cryo-electron microscopy. Nature 628, 47–56 (2024). https://doi.org/10.1038/s41586-024-07198-2

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