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Proc Natl Acad Sci U S A. 2017 Mar 21;114(12):3103-3108. doi: 10.1073/pnas.1621152114. Epub 2017 Mar 7.

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

Author information

1
Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030.
2
National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030.
3
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.
4
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139.
5
Department of Biological Sciences, Purdue University, West Lafayette, IN 47907.
6
Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030; wah@bcm.edu.

Abstract

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.

KEYWORDS:

P22; annotation; cryo-EM; model; structure

PMID:
28270620
PMCID:
PMC5373346
DOI:
10.1073/pnas.1621152114
[Indexed for MEDLINE]
Free PMC Article

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