Macromolecular assembly structures by comparative modeling and electron microscopy.
Advances in electron microscopy allow for structure determination of large biological machines at increasingly higher resolutions. A key step in this process is fitting component structures into the electron microscopy-derived density map of their assembly. Comparative modeling can contribute by providing atomic models of the components, via fold assignment, sequence-structure alignment, model building, and model assessment. All four stages of comparative modeling can also benefit from consideration of the density map. In this chapter, we describe numerous types of modeling problems restrained by a density map and available protocols for finding solutions. In particular, we provide detailed instructions for density map-guided modeling using the Integrative Modeling Platform (IMP), MODELLER, and UCSF Chimera.
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA. kerenl@salilab.org
Keren
K
Lasker
Javier A
JA
Velázquez-Muriel
Benjamin M
BM
Webb
Zheng
Z
Yang
Thomas E
TE
Ferrin
Andrej
A
Sali
D000595:Amino Acid Sequence; D018834:Chaperonin 60 / Q000737:chemistry; D004926:Escherichia coli / Q000737:chemistry; D029968:Escherichia coli Proteins / Q000737:chemistry; D046911:Macromolecular Substances / Q000737:chemistry*; D008854:Microscopy, Electron / Q000379:methods*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods
D018834:Chaperonin 60; D029968:Escherichia coli Proteins; D046911:Macromolecular Substances; D011506:Proteins