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Cryo-electron tomography pipeline for plasma membranes

Author

Listed:
  • Willy W. Sun

    (US National Institutes of Health)

  • Dennis J. Michalak

    (US National Institutes of Health)

  • Kem A. Sochacki

    (US National Institutes of Health)

  • Prasanthi Kunamaneni

    (US National Institutes of Health
    US National Institutes of Health)

  • Marco A. Alfonzo-Méndez

    (US National Institutes of Health)

  • Andreas M. Arnold

    (US National Institutes of Health)

  • Marie-Paule Strub

    (US National Institutes of Health)

  • Jenny E. Hinshaw

    (US National Institutes of Health)

  • Justin W. Taraska

    (US National Institutes of Health)

Abstract

Cryo-electron tomography (cryoET) provides sub-nanometer protein structure within the dense cellular environment. Existing sample preparation methods are insufficient at accessing the plasma membrane and its associated proteins. Here, we present a correlative cryo-electron tomography pipeline optimally suited to image large ultra-thin areas of isolated basal and apical plasma membranes. The pipeline allows for angstrom-scale structure determination with subtomogram averaging and employs a genetically encodable rapid chemically-induced electron microscopy visible tag for marking specific proteins within the complex cellular environment. The pipeline provides efficient, distributable, low-cost sample preparation and enables targeted structural studies of identified proteins at the plasma membrane of mammalian cells.

Suggested Citation

  • Willy W. Sun & Dennis J. Michalak & Kem A. Sochacki & Prasanthi Kunamaneni & Marco A. Alfonzo-Méndez & Andreas M. Arnold & Marie-Paule Strub & Jenny E. Hinshaw & Justin W. Taraska, 2025. "Cryo-electron tomography pipeline for plasma membranes," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-56045-z
    DOI: 10.1038/s41467-025-56045-z
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    References listed on IDEAS

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    1. Yun-Tao Liu & Heng Zhang & Hui Wang & Chang-Lu Tao & Guo-Qiang Bi & Z. Hong Zhou, 2022. "Isotropic reconstruction for electron tomography with deep learning," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    2. Patrick C. Hoffmann & Jan Philipp Kreysing & Iskander Khusainov & Maarten W. Tuijtel & Sonja Welsch & Martin Beck, 2022. "Structures of the eukaryotic ribosome and its translational states in situ," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    3. Leopold Kong & Kem A. Sochacki & Huaibin Wang & Shunming Fang & Bertram Canagarajah & Andrew D. Kehr & William J. Rice & Marie-Paule Strub & Justin W. Taraska & Jenny E. Hinshaw, 2018. "Cryo-EM of the dynamin polymer assembled on lipid membrane," Nature, Nature, vol. 560(7717), pages 258-262, August.
    4. Alexander Fotin & Yifan Cheng & Piotr Sliz & Nikolaus Grigorieff & Stephen C. Harrison & Tomas Kirchhausen & Thomas Walz, 2004. "Molecular model for a complete clathrin lattice from electron cryomicroscopy," Nature, Nature, vol. 432(7017), pages 573-579, December.
    5. Max Gemmer & Marten L. Chaillet & Joyce Loenhout & Rodrigo Cuevas Arenas & Dimitrios Vismpas & Mariska Gröllers-Mulderij & Fujiet A. Koh & Pascal Albanese & Richard A. Scheltema & Stuart C. Howes & Ab, 2023. "Visualization of translation and protein biogenesis at the ER membrane," Nature, Nature, vol. 614(7946), pages 160-167, February.
    6. Casper Berger & Maud Dumoux & Thomas Glen & Neville B.-y. Yee & John M. Mitchels & Zuzana Patáková & Michele C. Darrow & James H. Naismith & Michael Grange, 2023. "Plasma FIB milling for the determination of structures in situ," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    7. Joachim Frank & Rajendra Kumar Agrawal, 2000. "A ratchet-like inter-subunit reorganization of the ribosome during translocation," Nature, Nature, vol. 406(6793), pages 318-322, July.
    8. Nicholas I. Clarke & Stephen J. Royle, 2018. "FerriTag is a new genetically-encoded inducible tag for correlative light-electron microscopy," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
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