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Streamlined structure determination by cryo-electron tomography and subtomogram averaging using TomoBEAR

Author

Listed:
  • Nikita Balyschew

    (Max Planck Institute of Biophysics
    Goethe University of Frankfurt on Main)

  • Artsemi Yushkevich

    (Max Delbrück Center for Molecular Medicine in the Helmholtz Association
    Humboldt University of Berlin)

  • Vasilii Mikirtumov

    (Max Planck Institute of Biophysics
    Max Delbrück Center for Molecular Medicine in the Helmholtz Association)

  • Ricardo M. Sanchez

    (Max Planck Institute of Biophysics
    Goethe University of Frankfurt on Main
    EMBL Heidelberg)

  • Thiemo Sprink

    (Charité-Universitätsmedizin Berlin
    Cryo-EM Facility, Max Delbrück Center for Molecular Medicine in the Helmholtz Association)

  • Mikhail Kudryashev

    (Max Planck Institute of Biophysics
    Goethe University of Frankfurt on Main
    Max Delbrück Center for Molecular Medicine in the Helmholtz Association
    Charité-Universitätsmedizin Berlin)

Abstract

Structures of macromolecules in their native state provide unique unambiguous insights into their functions. Cryo-electron tomography combined with subtomogram averaging demonstrated the power to solve such structures in situ at resolutions in the range of 3 Angstrom for some macromolecules. In order to be applicable to the structural determination of the majority of macromolecules observable in cells in limited amounts, processing of tomographic data has to be performed in a high-throughput manner. Here we present TomoBEAR—a modular configurable workflow engine for streamlined processing of cryo-electron tomographic data for subtomogram averaging. TomoBEAR combines commonly used cryo-EM packages with reasonable presets to provide a transparent (“white box”) approach for data management and processing. We demonstrate applications of TomoBEAR to two data sets of purified macromolecular targets, to an ion channel RyR1 in a membrane, and the tomograms of plasma FIB-milled lamellae and demonstrate the ability to produce high-resolution structures. TomoBEAR speeds up data processing, minimizes human interventions, and will help accelerate the adoption of in situ structural biology by cryo-ET. The source code and the documentation are freely available.

Suggested Citation

  • Nikita Balyschew & Artsemi Yushkevich & Vasilii Mikirtumov & Ricardo M. Sanchez & Thiemo Sprink & Mikhail Kudryashev, 2023. "Streamlined structure determination by cryo-electron tomography and subtomogram averaging using TomoBEAR," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-42085-w
    DOI: 10.1038/s41467-023-42085-w
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    References listed on IDEAS

    as
    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. 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.
    3. Liang Xue & Swantje Lenz & Maria Zimmermann-Kogadeeva & Dimitry Tegunov & Patrick Cramer & Peer Bork & Juri Rappsilber & Julia Mahamid, 2022. "Visualizing translation dynamics at atomic detail inside a bacterial cell," Nature, Nature, vol. 610(7930), pages 205-211, October.
    4. Ricardo M. Sanchez & Yingyi Zhang & Wenbo Chen & Lea Dietrich & Mikhail Kudryashev, 2020. "Subnanometer-resolution structure determination in situ by hybrid subtomogram averaging - single particle cryo-EM," Nature Communications, Nature, vol. 11(1), pages 1-7, December.
    5. Liang Xue & Swantje Lenz & Maria Zimmermann-Kogadeeva & Dimitry Tegunov & Patrick Cramer & Peer Bork & Juri Rappsilber & Julia Mahamid, 2022. "Publisher Correction: Visualizing translation dynamics at atomic detail inside a bacterial cell," Nature, Nature, vol. 611(7937), pages 13-13, November.
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