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Structure. 2017 Apr 4;25(4):592-602.e2. doi: 10.1016/j.str.2017.02.004. Epub 2017 Mar 2.

Variability of Protein Structure Models from Electron Microscopy.

Author information

1
Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
2
Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; School of Pharmacy, Kitasato University, Minato-ku, Tokyo 108-8641, Japan.
3
Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA. Electronic address: dkihara@purdue.edu.

Abstract

An increasing number of biomolecular structures are solved by electron microscopy (EM). However, the quality of structure models determined from EM maps vary substantially. To understand to what extent structure models are supported by information embedded in EM maps, we used two computational structure refinement methods to examine how much structures can be refined using a dataset of 49 maps with accompanying structure models. The extent of structure modification as well as the disagreement between refinement models produced by the two computational methods scaled inversely with the global and the local map resolutions. A general quantitative estimation of deviations of structures for particular map resolutions are provided. Our results indicate that the observed discrepancy between the deposited map and the refined models is due to the lack of structural information present in EM maps and thus these annotations must be used with caution for further applications.

KEYWORDS:

EMDB; computational modelling; cryo-EM; electron microscopy; model refinement; protein structure modelling; protein tertiary structure; structure biology; structure optimization

PMID:
28262392
PMCID:
PMC5382112
DOI:
10.1016/j.str.2017.02.004
[Indexed for MEDLINE]
Free PMC Article

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