Accurate model annotation of a near-atomic resolution cryo-EM map

Hryc, Corey F.; Chen, Dong-Hua; Afonine, Pavel V.; Jakana, Joanita; Wang, Zhao; Haase-Pettingell, Cameron; Jiang, Wen; Adams, Paul D.; King, Jonathan A.; Schmid, Michael F.; Chiu, Wah

doi:10.1073/pnas.1621152114

Title: Accurate model annotation of a near-atomic resolution cryo-EM map

Journal Article · Tue Mar 07 00:00:00 EST 2017 · Proceedings of the National Academy of Sciences of the United States of America

DOI:https://doi.org/10.1073/pnas.1621152114· OSTI ID:1379782

Hryc, Corey F. ^[1]; Chen, Dong-Hua ^[2]; Afonine, Pavel V. ^[3]; Jakana, Joanita ^[2]; Wang, Zhao ^[2]; Haase-Pettingell, Cameron ^[4]; Jiang, Wen ^[5]; Adams, Paul D. ^[3]; King, Jonathan A. ^[4]; Schmid, Michael F. ^[6]; Chiu, Wah ^[6]

Baylor College of Medicine, Houston, TX (United States). Graduate Program in Structural and Computational Biology and Molecular Biophysics
Baylor College of Medicine, Houston, TX (United States). National Center for Macromolecular Imaging, Verna and Marrs McLean Dept. of Biochemistry and Molecular Biology
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division
Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Dept. of Biology
Purdue Univ., West Lafayette, IN (United States). Dept. of Biological Sciences
Baylor College of Medicine, Houston, TX (United States). Graduate Program in Structural and Computational Biology and Molecular Biophysics; Baylor College of Medicine, Houston, TX (United States). National Center for Macromolecular Imaging, Verna and Marrs McLean Dept. of Biochemistry and Molecular Biology

Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo- EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structural features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages.

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

Sponsoring Organization:: USDOE; National Institutes of Health (NIH); Robert Welch Foundation

Grant/Contract Number:: AC02-05CH11231; P01GM063210; P41GM103832; R01GM079429; PN2EY016525; T15LM007093

OSTI ID:: 1379782

Journal Information:: Proceedings of the National Academy of Sciences of the United States of America, Vol. 114, Issue 12; ISSN 0027-8424

Publisher:: National Academy of Sciences, Washington, DC (United States)Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 82 works

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Title: Accurate model annotation of a near-atomic resolution cryo-EM map

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