IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-024-55767-w.html
   My bibliography  Save this article

MPicker: visualizing and picking membrane proteins for cryo-electron tomography

Author

Listed:
  • Xiaofeng Yan

    (Tsinghua University
    Tsinghua University
    Tsinghua-Peking Joint Center for Life Sciences
    Beijing Frontier Research Center for Biological Structure)

  • Shudong Li

    (Tsinghua University
    Tsinghua University)

  • Weilin Huang

    (Tsinghua University
    Tsinghua University
    Tsinghua-Peking Joint Center for Life Sciences
    Beijing Frontier Research Center for Biological Structure)

  • Hao Wang

    (Tsinghua University
    Tsinghua University
    Tsinghua-Peking Joint Center for Life Sciences
    Beijing Frontier Research Center for Biological Structure)

  • Tianfang Zhao

    (Tsinghua University
    Tsinghua University
    Tsinghua-Peking Joint Center for Life Sciences
    Beijing Frontier Research Center for Biological Structure)

  • Mingtao Huang

    (Tsinghua University
    Tsinghua University
    Tsinghua-Peking Joint Center for Life Sciences
    Beijing Frontier Research Center for Biological Structure)

  • Niyun Zhou

    (Tsinghua University)

  • Yuan Shen

    (Tsinghua University
    Tsinghua University)

  • Xueming Li

    (Tsinghua University
    Tsinghua University
    Tsinghua-Peking Joint Center for Life Sciences
    Beijing Frontier Research Center for Biological Structure)

Abstract

Advancements in cryo-electron tomography (cryoET) allow the structure of macromolecules to be determined in situ, which is crucial for studying membrane protein structures and their interactions in the cellular environment. However, membranes are often highly curved and have a strong contrast in cryoET tomograms, which masks the signals from membrane proteins. These factors pose difficulties in observing and revealing the structures of membrane proteins in situ. Here, we report a membrane-flattening method and the corresponding software, MPicker, designed for the visualization, localization, and orientation determination of membrane proteins in cryoET tomograms. This method improves the visualization of proteins on and around membranes by generating a flattened tomogram that eliminates membrane curvature and reduces the spatial complexity of membrane protein analysis. In MPicker, we integrated approaches for automated particle picking and coarse alignment of membrane proteins for sub-tomogram averaging. MPicker was tested on tomograms of various cells to evaluate the method for visualizing, picking, and analyzing membrane proteins.

Suggested Citation

  • Xiaofeng Yan & Shudong Li & Weilin Huang & Hao Wang & Tianfang Zhao & Mingtao Huang & Niyun Zhou & Yuan Shen & Xueming Li, 2025. "MPicker: visualizing and picking membrane proteins for cryo-electron tomography," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-024-55767-w
    DOI: 10.1038/s41467-024-55767-w
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-55767-w
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-024-55767-w?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. 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. Julia Peukes & Xiaoli Xiong & Simon Erlendsson & Kun Qu & William Wan & Leslie J. Calder & Oliver Schraidt & Susann Kummer & Stefan M. V. Freund & Hans-Georg Kräusslich & John A. G. Briggs, 2020. "The native structure of the assembled matrix protein 1 of influenza A virus," Nature, Nature, vol. 587(7834), pages 495-498, November.
    3. Liang Wang & Xin Wen & Zhengmao Wang & Zaisheng Lin & Chunhong Li & Huilin Zhou & Huimin Yu & Yuhan Li & Yifei Cheng & Yuling Chen & Geer Lou & Junmin Pan & Muqing Cao, 2022. "Ciliary transition zone proteins coordinate ciliary protein composition and ectosome shedding," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    4. Larissa Heinrich & Davis Bennett & David Ackerman & Woohyun Park & John Bogovic & Nils Eckstein & Alyson Petruncio & Jody Clements & Song Pang & C. Shan Xu & Jan Funke & Wyatt Korff & Harald F. Hess &, 2021. "Whole-cell organelle segmentation in volume electron microscopy," Nature, Nature, vol. 599(7883), pages 141-146, November.
    5. Xin You & Xing Zhang & Jing Cheng & Yanan Xiao & Jianfei Ma & Shan Sun & Xinzheng Zhang & Hong-Wei Wang & Sen-Fang Sui, 2023. "In situ structure of the red algal phycobilisome–PSII–PSI–LHC megacomplex," Nature, Nature, vol. 616(7955), pages 199-206, April.
    6. Xinyu Zhang & Tianfang Zhao & Jiansheng Chen & Yuan Shen & Xueming Li, 2022. "EPicker is an exemplar-based continual learning approach for knowledge accumulation in cryoEM particle picking," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    Full references (including those not matched with items on IDEAS)

    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. Bryan S. Sibert & Joseph Y. Kim & Jie E. Yang & Zunlong Ke & Christopher C. Stobart & Martin L. Moore & Elizabeth R. Wright, 2024. "Assembly of respiratory syncytial virus matrix protein lattice and its coordination with fusion glycoprotein trimers," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Simon Wiedemann & Reinhard Heckel, 2024. "A deep learning method for simultaneous denoising and missing wedge reconstruction in cryogenic electron tomography," 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.
    4. Liming Zheng & Jie Xu & Weihua Wang & Xiaoyin Gao & Chao Zhao & Weijun Guo & Luzhao Sun & Hang Cheng & Fanhao Meng & Buhang Chen & Weiyu Sun & Xia Jia & Xiong Zhou & Kai Wu & Zhongfan Liu & Feng Ding , 2024. "Self-assembled superstructure alleviates air-water interface effect in cryo-EM," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    5. Zhiyuan Mao & Xingyue Li & Zhenhua Li & Liangliang Shen & Xiaoyi Li & Yanyan Yang & Wenda Wang & Tingyun Kuang & Jian-Ren Shen & Guangye Han, 2024. "Structure and distinct supramolecular organization of a PSII-ACPII dimer from a cryptophyte alga Chroomonas placoidea," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    6. Xia Li & Feng Qiao & Jiansheng Guo & Ting Jiang & Huifang Lou & Huixia Li & Gangcai Xie & Hangjun Wu & Weizhen Wang & Ruoyu Pei & Sha Liu & Mei Ye & Jin Li & Shiqin Huang & Mengya Zhang & Chaoye Ma & , 2025. "In situ architecture of the intercellular organelle reservoir between epididymal epithelial cells by volume electron microscopy," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    7. Weria Pezeshkian & John H. Ipsen, 2024. "Mesoscale simulation of biomembranes with FreeDTS," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    8. Xing Zhang & Yanan Xiao & Xin You & Shan Sun & Sen-Fang Sui, 2024. "In situ structural determination of cyanobacterial phycobilisome–PSII supercomplex by STAgSPA strategy," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    9. Iskander Khusainov & Natalie Romanov & Camille Goemans & Beata Turoňová & Christian E. Zimmerli & Sonja Welsch & Julian D. Langer & Athanasios Typas & Martin Beck, 2024. "Bactericidal effect of tetracycline in E. coli strain ED1a may be associated with ribosome dysfunction," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    10. Ravi Chawla & Jenna K. A. Tom & Tumara Boyd & Nicholas H. Tu & Tanxi Bai & Danielle A. Grotjahn & Donghyun Park & Ashok A. Deniz & Lisa R. Racki, 2024. "Reentrant DNA shells tune polyphosphate condensate size," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    11. Rebeccah A. Warmack & Ailiena O. Maggiolo & Andres Orta & Belinda B. Wenke & James B. Howard & Douglas C. Rees, 2023. "Structural consequences of turnover-induced homocitrate loss in nitrogenase," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    12. 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.
    13. 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.
    14. Hanh M. Truong & Kevin O. Cruz-Colón & Jorge Y. Martínez-Márquez & Jason R. Willer & Amanda M. Travis & Sondip K. Biswas & Woo-Kuen Lo & Hanno J. Bolz & Jillian N. Pearring, 2023. "The tectonic complex regulates membrane protein composition in the photoreceptor cilium," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    15. Tim Schulte & Antonio Chaves-Sanjuan & Valentina Speranzini & Kevin Sicking & Melissa Milazzo & Giulia Mazzini & Paola Rognoni & Serena Caminito & Paolo Milani & Chiara Marabelli & Alessandro Corbelli, 2024. "Helical superstructures between amyloid and collagen in cardiac fibrils from a patient with AL amyloidosis," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    16. Chixiang Lu & Kai Chen & Heng Qiu & Xiaojun Chen & Gu Chen & Xiaojuan Qi & Haibo Jiang, 2024. "Diffusion-based deep learning method for augmenting ultrastructural imaging and volume electron microscopy," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    17. Yang Huang & Feibo Song & Yuanjun Zeng & Hui Sun & Roufang Sheng & Xuechun Wang & Liqin Liu & Guoxing Luo & Yanan Jiang & Yaling Chen & Mengxuan Zhang & Shiyin Zhang & Ying Gu & Hai Yu & Shaowei Li & , 2025. "A single residue switch mediates the broad neutralization of Rotaviruses," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    18. Xueming Meng & Cong Xu & Jiawei Li & Benhua Qiu & Jiajun Luo & Qin Hong & Yujie Tong & Chuyu Fang & Yanyan Feng & Rui Ma & Xiangyi Shi & Cheng Lin & Chen Pan & Xueliang Zhu & Xiumin Yan & Yao Cong, 2024. "Multi-scale structures of the mammalian radial spoke and divergence of axonemal complexes in ependymal cilia," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    19. Kang Zhou & Zhu Si & Peng Ge & Jun Tsao & Ming Luo & Z. Hong Zhou, 2022. "Atomic model of vesicular stomatitis virus and mechanism of assembly," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    20. Long-Sheng Zhao & Ning Wang & Kang Li & Chun-Yang Li & Jian-Ping Guo & Fei-Yu He & Gui-Ming Liu & Xiu-Lan Chen & Jun Gao & Lu-Ning Liu & Yu-Zhong Zhang, 2024. "Architecture of symbiotic dinoflagellate photosystem I–light-harvesting supercomplex in Symbiodinium," Nature Communications, Nature, vol. 15(1), pages 1-13, 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:16:y:2025:i:1:d:10.1038_s41467-024-55767-w. 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.