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An atomic model of brome mosaic virus using direct electron detection and real-space optimization

Author

Listed:
  • Zhao Wang

    (National Center for Macromolecular Imaging, Baylor College of Medicine)

  • Corey F. Hryc

    (National Center for Macromolecular Imaging, Baylor College of Medicine
    Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine)

  • Benjamin Bammes

    (Direct Electron LP)

  • Pavel V. Afonine

    (Lawrence Berkeley National Laboratory)

  • Joanita Jakana

    (National Center for Macromolecular Imaging, Baylor College of Medicine)

  • Dong-Hua Chen

    (National Center for Macromolecular Imaging, Baylor College of Medicine)

  • Xiangan Liu

    (National Center for Macromolecular Imaging, Baylor College of Medicine)

  • Matthew L. Baker

    (National Center for Macromolecular Imaging, Baylor College of Medicine)

  • Cheng Kao

    (Indiana University)

  • Steven J. Ludtke

    (National Center for Macromolecular Imaging, Baylor College of Medicine
    Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine)

  • Michael F. Schmid

    (National Center for Macromolecular Imaging, Baylor College of Medicine
    Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine)

  • Paul D. Adams

    (Lawrence Berkeley National Laboratory
    University of California)

  • Wah Chiu

    (National Center for Macromolecular Imaging, Baylor College of Medicine
    Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine)

Abstract

Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bias and overfitting. Here we describe a complete workflow for data acquisition, image processing, all-atom modelling and validation of brome mosaic virus, an RNA virus. Data were collected with a direct electron detector in integrating mode and an exposure beyond the traditional radiation damage limit. The final density map has a resolution of 3.8 Å as assessed by two independent data sets and maps. We used the map to derive an all-atom model with a newly implemented real-space optimization protocol. The validity of the model was verified by its match with the density map and a previous model from X-ray crystallography, as well as the internal consistency of models from independent maps. This study demonstrates a practical approach to obtain a rigorously validated atomic resolution electron cryo-microscopy structure.

Suggested Citation

  • Zhao Wang & Corey F. Hryc & Benjamin Bammes & Pavel V. Afonine & Joanita Jakana & Dong-Hua Chen & Xiangan Liu & Matthew L. Baker & Cheng Kao & Steven J. Ludtke & Michael F. Schmid & Paul D. Adams & Wa, 2014. "An atomic model of brome mosaic virus using direct electron detection and real-space optimization," Nature Communications, Nature, vol. 5(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms5808
    DOI: 10.1038/ncomms5808
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    Cited by:

    1. Jingjing Wang & Meng Wu & Zhangcheng Chen & Lijie Wu & Tian Wang & Dongmei Cao & Huan Wang & Shenhui Liu & Yueming Xu & Fei Li & Junlin Liu & Na Chen & Suwen Zhao & Jianjun Cheng & Sheng Wang & Tian H, 2022. "The unconventional activation of the muscarinic acetylcholine receptor M4R by diverse ligands," Nature Communications, Nature, vol. 13(1), pages 1-10, December.

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