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

Wang, Zhao; Hryc, Corey F.; Bammes, Benjamin; Afonine, Pavel V.; Jakana, Joanita; Chen, Dong-Hua; Liu, Xiangan; Baker, Matthew L.; Kao, Cheng; Ludtke, Steven J.; Schmid, Michael F.; Adams, Paul D.; Chiu, Wah

doi:10.1038/ncomms5808

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

Journal Article · Thu Sep 04 00:00:00 EDT 2014 · Nature Communications

DOI:https://doi.org/10.1038/ncomms5808· OSTI ID:1623956

Wang, Zhao ^[1]; Hryc, Corey F. ^[2]; Bammes, Benjamin ^[3]; Afonine, Pavel V. ^[4]; Jakana, Joanita ^[1]; Chen, Dong-Hua ^[1]; Liu, Xiangan ^[1]; Baker, Matthew L. ^[1]; Kao, Cheng ^[5]; Ludtke, Steven J. ^[2]; Schmid, Michael F. ^[2]; Adams, Paul D. ^[6]; Chiu, Wah ^[2]

Baylor Univ., Houston, TX (United States). College of Medicine. Verna and Marrs McLean Dept. of Biochemistry and Molecular Biology. National Center for Macromolecular Imaging
Baylor Univ., Houston, TX (United States). College of Medicine. Verna and Marrs McLean Dept. of Biochemistry and Molecular Biology. National Center for Macromolecular Imaging; Baylor Univ., Houston, TX (United States). College of Medicine. Graduate Program in Structural and Computational Biology and Molecular Biophysics
Direct Electron LP, San Diego, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division
Indiana Univ., Bloomington, IN (United States). Dept. of Molecular and Cellular Biochemistry
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1623956

Journal Information:: Nature Communications, Vol. 5, Issue 1; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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