Analyses of subnanometer resolution cryo-EM density maps

Methods Enzymol. 2010;483:1-29. doi: 10.1016/S0076-6879(10)83001-0.

Abstract

Today, electron cryomicroscopy (cryo-EM) can routinely achieve subnanometer resolutions of complex macromolecular assemblies. From a density map, one can extract key structural and functional information using a variety of computational analysis tools. At subnanometer resolution, these tools make it possible to isolate individual subunits, identify secondary structures, and accurately fit atomic models. With several cryo-EM studies achieving resolutions beyond 5Å, computational modeling and feature recognition tools have been employed to construct backbone and atomic models of the protein components directly from a density map. In this chapter, we describe several common classes of computational tools that can be used to analyze and model subnanometer resolution reconstructions from cryo-EM. A general protocol for analyzing subnanometer resolution density maps is presented along with a full description of steps used in analyzing the 4.3Å resolution structure of Mm-cpn.

Publication types

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

MeSH terms

  • Computer Simulation
  • Cryoelectron Microscopy / methods*
  • Group II Chaperonins / chemistry
  • Image Processing, Computer-Assisted
  • Models, Molecular
  • Protein Conformation
  • Protein Structure, Secondary

Substances

  • Group II Chaperonins