IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v11y2020i1d10.1038_s41467-020-17466-0.html
   My bibliography  Save this article

Subnanometer-resolution structure determination in situ by hybrid subtomogram averaging - single particle cryo-EM

Author

Listed:
  • Ricardo M. Sanchez

    (Max Planck Institute for Biophysics
    Goethe University of Frankfurt am Main)

  • Yingyi Zhang

    (Max Planck Institute for Biophysics
    Goethe University of Frankfurt am Main)

  • Wenbo Chen

    (Max Planck Institute for Biophysics
    Goethe University of Frankfurt am Main)

  • Lea Dietrich

    (Max Planck Institute for Biophysics)

  • Mikhail Kudryashev

    (Max Planck Institute for Biophysics
    Goethe University of Frankfurt am Main)

Abstract

Cryo-electron tomography combined with subtomogram averaging (StA) has yielded high-resolution structures of macromolecules in their native context. However, high-resolution StA is not commonplace due to beam-induced sample drift, images with poor signal-to-noise ratios (SNR), challenges in CTF correction, and limited particle number. Here we address these issues by collecting tilt series with a higher electron dose at the zero-degree tilt. Particles of interest are then located within reconstructed tomograms, processed by conventional StA, and then re-extracted from the high-dose images in 2D. Single particle analysis tools are then applied to refine the 2D particle alignment and generate a reconstruction. Use of our hybrid StA (hStA) workflow improved the resolution for tobacco mosaic virus from 7.2 to 4.4 Å and for the ion channel RyR1 in crowded native membranes from 12.9 to 9.1 Å. These resolution gains make hStA a promising approach for other StA projects aimed at achieving subnanometer resolution.

Suggested Citation

  • 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.
  • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-17466-0
    DOI: 10.1038/s41467-020-17466-0
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-020-17466-0
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-020-17466-0?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. 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.
    2. Yanan Zhu & Christopher W. Koo & C. Keith Cassidy & Matthew C. Spink & Tao Ni & Laura C. Zanetti-Domingues & Benji Bateman & Marisa L. Martin-Fernandez & Juan Shen & Yuewen Sheng & Yun Song & Zhengyi , 2022. "Structure and activity of particulate methane monooxygenase arrays in methanotrophs," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    3. Shouwen Du & Ruchao Peng & Wang Xu & Xiaoyun Qu & Yuhang Wang & Jiamin Wang & Letian Li & Mingyao Tian & Yudong Guan & Jigang Wang & Guoqing Wang & Hao Li & Lingcong Deng & Xiaoshuang Shi & Yidan Ma &, 2023. "Cryo-EM structure of severe fever with thrombocytopenia syndrome virus," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    4. Kotaro Kelley & Ashleigh M. Raczkowski & Oleg Klykov & Pattana Jaroenlak & Daija Bobe & Mykhailo Kopylov & Edward T. Eng & Gira Bhabha & Clinton S. Potter & Bridget Carragher & Alex J. Noble, 2022. "Waffle Method: A general and flexible approach for improving throughput in FIB-milling," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    5. Jing Cheng & Tong Liu & Xin You & Fa Zhang & Sen-Fang Sui & Xiaohua Wan & Xinzheng Zhang, 2023. "Determining protein structures in cellular lamella at pseudo-atomic resolution by GisSPA," Nature Communications, Nature, vol. 14(1), pages 1-9, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-17466-0. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.