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

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 and Wah Chiu ()
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Zhao Wang: National Center for Macromolecular Imaging, Baylor College of Medicine
Corey F. Hryc: National Center for Macromolecular Imaging, 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
Michael F. Schmid: National Center for Macromolecular Imaging, Baylor College of Medicine
Paul D. Adams: Lawrence Berkeley National Laboratory
Wah Chiu: National Center for Macromolecular Imaging, Baylor College of Medicine

Nature Communications, 2014, vol. 5, issue 1, 1-12

Abstract: 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.

Date: 2014
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DOI: 10.1038/ncomms5808

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