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Pushing the resolution limit by correcting the Ewald sphere effect in single-particle Cryo-EM reconstructions

Author

Listed:
  • Dongjie Zhu

    (Chinese Academy of Sciences
    University of Science and Technology of China)

  • Xiangxi Wang

    (Chinese Academy of Sciences)

  • Qianglin Fang

    (Purdue University)

  • James L Etten

    (University of Nebraska)

  • Michael G Rossmann

    (Purdue University)

  • Zihe Rao

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences
    Tsinghua University)

  • Xinzheng Zhang

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences
    Chinese Academy of Sciences)

Abstract

The Ewald sphere effect is generally neglected when using the Central Projection Theorem for cryo electron microscopy single-particle reconstructions. This can reduce the resolution of a reconstruction. Here we estimate the attainable resolution and report a “block-based” reconstruction method for extending the resolution limit. We find the Ewald sphere effect limits the resolution of large objects, especially large viruses. After processing two real datasets of large viruses, we show that our procedure can extend the resolution for both datasets and can accommodate the flexibility associated with large protein complexes.

Suggested Citation

  • Dongjie Zhu & Xiangxi Wang & Qianglin Fang & James L Etten & Michael G Rossmann & Zihe Rao & Xinzheng Zhang, 2018. "Pushing the resolution limit by correcting the Ewald sphere effect in single-particle Cryo-EM reconstructions," Nature Communications, Nature, vol. 9(1), pages 1-7, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-04051-9
    DOI: 10.1038/s41467-018-04051-9
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    Cited by:

    1. Qi Jia & Ye Xiang, 2023. "Cryo-EM structure of a bacteriophage M13 mini variant," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Duanfang Cao & Bingting Ma & Ziyi Cao & Xiaoyu Xu & Xinzheng Zhang & Ye Xiang, 2024. "The receptor VLDLR binds Eastern Equine Encephalitis virus through multiple distinct modes," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    3. Yashan Yang & Qianqian Shao & Mingcheng Guo & Lin Han & Xinyue Zhao & Aohan Wang & Xiangyun Li & Bo Wang & Ji-An Pan & Zhenguo Chen & Andrei Fokine & Lei Sun & Qianglin Fang, 2024. "Capsid structure of bacteriophage ΦKZ provides insights into assembly and stabilization of jumbo phages," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    4. Guosong Wang & Zhenghui Zha & Pengfei Huang & Hui Sun & Yang Huang & Maozhou He & Tian Chen & Lina Lin & Zhenqin Chen & Zhibo Kong & Yuqiong Que & Tingting Li & Ying Gu & Hai Yu & Jun Zhang & Qingbing, 2022. "Structures of pseudorabies virus capsids," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    5. Qianqian Shao & Irina V. Agarkova & Eric A. Noel & David D. Dunigan & Yunshu Liu & Aohan Wang & Mingcheng Guo & Linlin Xie & Xinyue Zhao & Michael G. Rossmann & James L. Etten & Thomas Klose & Qiangli, 2022. "Near-atomic, non-icosahedrally averaged structure of giant virus Paramecium bursaria chlorella virus 1," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    6. 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.
    7. Rong-Cheng Yu & Feng Yang & Hong-Yan Zhang & Pu Hou & Kang Du & Jie Zhu & Ning Cui & Xudong Xu & Yuxing Chen & Qiong Li & Cong-Zhao Zhou, 2024. "Structure of the intact tail machine of Anabaena myophage A-1(L)," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    8. Zhennan Zhao & Youhua Huang & Congcong Liu & Dongjie Zhu & Shuaixin Gao & Sheng Liu & Ruchao Peng & Ya Zhang & Xiaohong Huang & Jianxun Qi & Catherine C. L. Wong & Xinzheng Zhang & Peiyi Wang & Qiwei , 2023. "Near-atomic architecture of Singapore grouper iridovirus and implications for giant virus assembly," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

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