Variability of Protein Structure Models from Electron Microscopy

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


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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, N.I.H., Extramural

MeSH terms

  • Computational Biology / methods*
  • Cryoelectron Microscopy / methods*
  • Databases, Protein
  • Models, Molecular
  • Protein Conformation
  • Proteins / chemistry*
  • Proteins / ultrastructure


  • Proteins