Electron cryomicroscopy of biological machines at subnanometer resolution.
Advances in electron cryomicroscopy (cryo-EM) have made possible the structural determination of large biological machines in the resolution range of 6-9 angstroms. Rice dwarf virus and the acrosomal bundle represent two distinct types of machines amenable to cryo-EM investigations at subnanometer resolutions. However, calculating the density map is only the first step, and much analysis remains to extract structural insights and the mechanism of action in these machines. This paper will review the computational and visualization methodologies necessary for analysis (structure mining) of the computed cryo-EM maps of these machines. These steps include component segmentation, averaging based on local symmetry among components, density connectivity trace, incorporation of bioinformatics analysis, and fitting of high-resolution component data, if available. The consequences of these analyses can not only identify accurately some of the secondary structure elements of the molecular components in machines but also suggest structural mechanisms related to their biological functions.
Chiu
Wah
W
National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA. wah@bcm.tmc.edu
Baker
Matthew L
ML
Jiang
Wen
W
Dougherty
Matthew
M
Schmid
Michael F
MF
D036022:Capsid Proteins / Q000737:chemistry; D020285:Cryoelectron Microscopy; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry*; D049329:Nanostructures / Q000737:chemistry; D017433:Protein Structure, Secondary; D014780:Viruses / Q000737:chemistry
D036022:Capsid Proteins; D046912:Multiprotein Complexes