Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock
Fig 5
Docking and characterization of one- and two-component polyhedral assemblies using RPXDock.
A. Models of one- and two-component docked polyhedral assemblies with the oligomeric building blocks in purple and orange. The asymmetric unit of each assembly, comprising one subunit of each building block, is colored dark purple and dark orange. B. Reference-free 2D class averages from negative stain electron microscopy. Each assembly is viewed along several axes of symmetry. C. 3D density maps reconstructed from selected 2D class averages. D. Overlays of each design model fit into its 3D density map, confirming that each design assembles to the architecture identified by RPXDock. E. Characterization of the two-component octahedral assembly O43-rpxdock-EK1 by cryogenic electron microscopy. The design model is colored as in A). To the right are representative 2D class averages showing different axes of symmetry and a reconstructed 3D map at 3.7 Å resolution. The overlay of the original dock (orange and purple) with the model built from the 3D reconstruction (gray) shows 4 Å Cα root mean square deviation between the original dock and cryoEM structure over 48 chains.