Improving the Accuracy of Fitted Atomic Models in Cryo-EM Density Maps of Protein Assemblies Using Evolutionary Information From Aligned Homologous Proteins

Methods Mol Biol. 2016;1415:193-209. doi: 10.1007/978-1-4939-3572-7_10.


Cryo-Electron Microscopy (cryo-EM) has become an important technique to obtain structural insights into large macromolecular assemblies. However the resolution of the density maps do not allow for its interpretation at atomic level. Hence they are combined with high resolution structures along with information from other experimental or bioinformatics techniques to obtain pseudo-atomic models. Here, we describe the use of evolutionary conservation of residues as obtained from protein structures and alignments of homologous proteins to detect errors in the fitting of atomic structures as well as improve accuracy of the protein-protein interfacial regions in the cryo-EM density maps.

Keywords: Evolutionary conservation; Protein structure and sequence alignments; Protein-protein complexes; cryo-EM; cryo-EM density fitting.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Conserved Sequence
  • Cryoelectron Microscopy / methods*
  • Evolution, Molecular
  • Models, Molecular
  • Molecular Docking Simulation
  • Multiprotein Complexes / chemistry*
  • Protein Binding
  • Protein Conformation
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Structural Homology, Protein


  • Multiprotein Complexes