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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