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Cryogenic electron ptychographic single particle analysis with wide bandwidth information transfer

Author

Listed:
  • Xudong Pei

    (Nanjing University)

  • Liqi Zhou

    (Nanjing University
    University of Warwick)

  • Chen Huang

    (Harwell Science and Innovation Campus)

  • Mark Boyce

    (University of Oxford)

  • Judy S. Kim

    (Harwell Science and Innovation Campus
    University of Oxford)

  • Emanuela Liberti

    (Harwell Science and Innovation Campus)

  • Yiming Hu

    (Nanjing University)

  • Takeo Sasaki

    (JEOL Ltd)

  • Peter D. Nellist

    (University of Oxford)

  • Peijun Zhang

    (University of Oxford
    Harwell Science and Innovation Campus)

  • David I. Stuart

    (University of Oxford
    Harwell Science and Innovation Campus)

  • Angus I. Kirkland

    (Harwell Science and Innovation Campus
    University of Oxford
    Harwell Science and Innovation Campus)

  • Peng Wang

    (Nanjing University
    University of Warwick)

Abstract

Advances in cryogenic transmission electron microscopy have revolutionised the determination of many macromolecular structures at atomic or near-atomic resolution. This method is based on conventional defocused phase contrast imaging. However, it has limitations of weaker contrast for small biological molecules embedded in vitreous ice, in comparison with cryo-ptychography, which shows increased contrast. Here we report a single-particle analysis based on the use of ptychographic reconstruction data, demonstrating that three dimensional reconstructions with a wide information transfer bandwidth can be recovered by Fourier domain synthesis. Our work suggests future applications in otherwise challenging single particle analyses, including small macromolecules and heterogeneous or flexible particles. In addition structure determination in situ within cells without the requirement for protein purification and expression may be possible.

Suggested Citation

  • Xudong Pei & Liqi Zhou & Chen Huang & Mark Boyce & Judy S. Kim & Emanuela Liberti & Yiming Hu & Takeo Sasaki & Peter D. Nellist & Peijun Zhang & David I. Stuart & Angus I. Kirkland & Peng Wang, 2023. "Cryogenic electron ptychographic single particle analysis with wide bandwidth information transfer," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-38268-0
    DOI: 10.1038/s41467-023-38268-0
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    References listed on IDEAS

    as
    1. Yi Jiang & Zhen Chen & Yimo Han & Pratiti Deb & Hui Gao & Saien Xie & Prafull Purohit & Mark W. Tate & Jiwoong Park & Sol M. Gruner & Veit Elser & David A. Muller, 2018. "Electron ptychography of 2D materials to deep sub-ångström resolution," Nature, Nature, vol. 559(7714), pages 343-349, July.
    2. H. Yang & R. N. Rutte & L. Jones & M. Simson & R. Sagawa & H. Ryll & M. Huth & T. J. Pennycook & M.L.H. Green & H. Soltau & Y. Kondo & B. G. Davis & P. D. Nellist, 2016. "Simultaneous atomic-resolution electron ptychography and Z-contrast imaging of light and heavy elements in complex nanostructures," Nature Communications, Nature, vol. 7(1), pages 1-8, November.
    3. Si Gao & Peng Wang & Fucai Zhang & Gerardo T. Martinez & Peter D. Nellist & Xiaoqing Pan & Angus I. Kirkland, 2017. "Electron ptychographic microscopy for three-dimensional imaging," Nature Communications, Nature, vol. 8(1), pages 1-8, December.
    4. Martin Dierolf & Andreas Menzel & Pierre Thibault & Philipp Schneider & Cameron M. Kewish & Roger Wepf & Oliver Bunk & Franz Pfeiffer, 2010. "Ptychographic X-ray computed tomography at the nanoscale," Nature, Nature, vol. 467(7314), pages 436-439, September.
    5. Ka Man Yip & Niels Fischer & Elham Paknia & Ashwin Chari & Holger Stark, 2020. "Atomic-resolution protein structure determination by cryo-EM," Nature, Nature, vol. 587(7832), pages 157-161, November.
    6. Liqi Zhou & Jingdong Song & Judy S. Kim & Xudong Pei & Chen Huang & Mark Boyce & Luiza Mendonça & Daniel Clare & Alistair Siebert & Christopher S. Allen & Emanuela Liberti & David Stuart & Xiaoqing Pa, 2020. "Low-dose phase retrieval of biological specimens using cryo-electron ptychography," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
    7. Zhen Chen & Michal Odstrcil & Yi Jiang & Yimo Han & Ming-Hui Chiu & Lain-Jong Li & David A. Muller, 2020. "Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
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