IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-36372-9.html
   My bibliography  Save this article

Plasma FIB milling for the determination of structures in situ

Author

Listed:
  • Casper Berger

    (Harwell Science & Innovation Campus
    University of Oxford)

  • Maud Dumoux

    (Harwell Science & Innovation Campus)

  • Thomas Glen

    (Harwell Science & Innovation Campus)

  • Neville B.-y. Yee

    (Harwell Science & Innovation Campus)

  • John M. Mitchels

    (Thermo Fisher Scientific Brno s.r.o)

  • Zuzana Patáková

    (Thermo Fisher Scientific Brno s.r.o)

  • Michele C. Darrow

    (Harwell Science & Innovation Campus)

  • James H. Naismith

    (Harwell Science & Innovation Campus
    University of Oxford)

  • Michael Grange

    (Harwell Science & Innovation Campus
    University of Oxford)

Abstract

Structural biology studies inside cells and tissues require methods to thin vitrified specimens to electron transparency. Until now, focused ion beams based on gallium have been used. However, ion implantation, changes to surface chemistry and an inability to access high currents limit gallium application. Here, we show that plasma-coupled ion sources can produce cryogenic lamellae of vitrified human cells in a robust and automated manner, with quality sufficient for pseudo-atomic structure determination. Lamellae were produced in a prototype microscope equipped for long cryogenic run times (> 1 week) and with multi-specimen support fully compatible with modern-day transmission electron microscopes. We demonstrate that plasma ion sources can be used for structural biology within cells, determining a structure in situ to 4.9 Å, and characterise the resolution dependence on particle distance from the lamella edge. We describe a workflow upon which different plasmas can be examined to further streamline lamella fabrication.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-36372-9
    DOI: 10.1038/s41467-023-36372-9
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-36372-9
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-36372-9?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
    ---><---

    References listed on IDEAS

    as
    1. Geoff Sutton & Dapeng Sun & Xiaofeng Fu & Abhay Kotecha & Corey W. Hecksel & Daniel K. Clare & Peijun Zhang & David I. Stuart & Mark Boyce, 2020. "Assembly intermediates of orthoreovirus captured in the cell," Nature Communications, Nature, vol. 11(1), pages 1-7, December.
    2. Oleksiy Kovtun & Natalya Leneva & Yury S. Bykov & Nicholas Ariotti & Rohan D. Teasdale & Miroslava Schaffer & Benjamin D. Engel & David. J. Owen & John A. G. Briggs & Brett M. Collins, 2018. "Structure of the membrane-assembled retromer coat determined by cryo-electron tomography," Nature, Nature, vol. 561(7724), pages 561-564, September.
    3. Anthony P. Schuller & Matthias Wojtynek & David Mankus & Meltem Tatli & Rafael Kronenberg-Tenga & Saroj G. Regmi & Phat V. Dip & Abigail K. R. Lytton-Jean & Edward J. Brignole & Mary Dasso & Karsten W, 2021. "The cellular environment shapes the nuclear pore complex architecture," Nature, Nature, vol. 598(7882), pages 667-671, October.
    4. Heena Khatter & Alexander G. Myasnikov & S. Kundhavai Natchiar & Bruno P. Klaholz, 2015. "Structure of the human 80S ribosome," Nature, Nature, vol. 520(7549), pages 640-645, April.
    5. Matteo Allegretti & Christian E. Zimmerli & Vasileios Rantos & Florian Wilfling & Paolo Ronchi & Herman K. H. Fung & Chia-Wei Lee & Wim Hagen & Beata Turoňová & Kai Karius & Mandy Börmel & Xiaojie Zha, 2020. "In-cell architecture of the nuclear pore and snapshots of its turnover," Nature, Nature, vol. 586(7831), pages 796-800, October.
    Full references (including those not matched with items on IDEAS)

    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. Benjamin C. Creekmore & Kathryn Kixmoeller & Ben E. Black & Edward B. Lee & Yi-Wei Chang, 2024. "Ultrastructure of human brain tissue vitrified from autopsy revealed by cryo-ET with cryo-plasma FIB milling," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    3. Zhen Hou & Frank Nightingale & Yanan Zhu & Craig MacGregor-Chatwin & Peijun Zhang, 2023. "Structure of native chromatin fibres revealed by Cryo-ET in situ," Nature Communications, Nature, vol. 14(1), pages 1-7, December.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Patrick Bryant & Gabriele Pozzati & Wensi Zhu & Aditi Shenoy & Petras Kundrotas & Arne Elofsson, 2022. "Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    2. Gabriel Therizols & Zeina Bash-Imam & Baptiste Panthu & Christelle Machon & Anne Vincent & Julie Ripoll & Sophie Nait-Slimane & Mounira Chalabi-Dchar & Angéline Gaucherot & Maxime Garcia & Florian Laf, 2022. "Alteration of ribosome function upon 5-fluorouracil treatment favors cancer cell drug-tolerance," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    3. Fabrizio A. Pennacchio & Alessandro Poli & Francesca Michela Pramotton & Stefania Lavore & Ilaria Rancati & Mario Cinquanta & Daan Vorselen & Elisabetta Prina & Orso Maria Romano & Aldo Ferrari & Matt, 2024. "N2FXm, a method for joint nuclear and cytoplasmic volume measurements, unravels the osmo-mechanical regulation of nuclear volume in mammalian cells," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    4. Asaf Ashkenazy-Titelman & Mohammad Khaled Atrash & Alon Boocholez & Noa Kinor & Yaron Shav-Tal, 2022. "RNA export through the nuclear pore complex is directional," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    5. Sheung Chun Ng & Abin Biswas & Trevor Huyton & Jürgen Schünemann & Simone Reber & Dirk Görlich, 2023. "Barrier properties of Nup98 FG phases ruled by FG motif identity and inter-FG spacer length," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    6. 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.
    7. K. Shanmugha Rajan & Hava Madmoni & Anat Bashan & Masato Taoka & Saurav Aryal & Yuko Nobe & Tirza Doniger & Beathrice Galili Kostin & Amit Blumberg & Smadar Cohen-Chalamish & Schraga Schwartz & Andre , 2023. "A single pseudouridine on rRNA regulates ribosome structure and function in the mammalian parasite Trypanosoma brucei," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    8. Arthur A. Melo & Thiemo Sprink & Jeffrey K. Noel & Elena Vázquez-Sarandeses & Chris Hoorn & Saif Mohd & Justus Loerke & Christian M. T. Spahn & Oliver Daumke, 2022. "Cryo-electron tomography reveals structural insights into the membrane remodeling mode of dynamin-like EHD filaments," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    9. Maximilian Seidel & Anja Becker & Filipa Pereira & Jonathan J. M. Landry & Nayara Trevisan Doimo Azevedo & Claudia M. Fusco & Eva Kaindl & Natalie Romanov & Janina Baumbach & Julian D. Langer & Erin M, 2022. "Co-translational assembly orchestrates competing biogenesis pathways," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    10. Chengwei Zeng & Yiren Jian & Soroush Vosoughi & Chen Zeng & Yunjie Zhao, 2023. "Evaluating native-like structures of RNA-protein complexes through the deep learning method," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
    11. David Winogradoff & Han-Yi Chou & Christopher Maffeo & Aleksei Aksimentiev, 2022. "Percolation transition prescribes protein size-specific barrier to passive transport through the nuclear pore complex," Nature Communications, Nature, vol. 13(1), pages 1-16, 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:14:y:2023:i:1:d:10.1038_s41467-023-36372-9. 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.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with 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.