Modeling of a 14 kDa RUVBL2-Binding Domain with Medium Resolution Cryo-EM Density

• DOI: 10.1021/acs.jcim.9b01095
• Publication Date: 2020-03-16T14:05:15Z
• Authors: Carlos F. Rodríguez; Mohinder Pal; Hugo Muñoz-Hernandez; Laurence H. Pearl; Oscar Llorca
• Keywords: Cryo-Electron Microscopy

The number of high-resolution structures protein complexes obtained using cryo-electron microscopy (cryo-EM) is increasing rapidly. Cryo-EM maps large macromolecular frequently contain regions resolved at different resolution levels, and modeling atomic de novo can be difficult for domains determined worse than 5 Å in the absence information from other structures. Here we describe details step-by-step decisions strategy followed to model RUVBL2-binding domain (RBD), a 14 kDa C-terminus RNA Polymerase II associated 3 (RPAP3) which was not available. Modeling performed on cryo-EM map 4.0–5.5 resolution, integrating secondary structure predictions, homology modeling, restraints cross-linked mass spectrometry, molecular dynamics (MD) AMBER. Here, compare our with RBD by NMR evaluate strategy. We also perform new MD simulations important residues mediating interaction RUVBL2 analyze their conservation homologous domains. Our approach its evaluation serve as an example address analysis medium maps.