title: Analyses of subnanometer resolution cryo-EM density maps.
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.
authors.affiliation: National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA.
authors.forename: Matthew L
authors.initials: ML
authors.lastname: Baker
authors.forename: Mariah R
authors.initials: MR
authors.lastname: Baker
authors.forename: Corey F
authors.initials: CF
authors.lastname: Hryc
authors.forename: Frank
authors.initials: F
authors.lastname: Dimaio
mesh_terms: D003198:Computer Simulation; D020285:Cryoelectron Microscopy / Q000379:methods*; D056385:Group II Chaperonins / Q000737:chemistry; D007091:Image Processing, Computer-Assisted; D008958:Models, Molecular; D011487:Protein Conformation; D017433:Protein Structure, Secondary
chemical_list: D056385:Group II Chaperonins