FIG 8.

Refitting MAb A6.2 Fab structure into the cryo-TEM for Fab-virus interaction. With the crystal structures of both the Fab and the P domain determined, the fitting of the structures into the molecular envelopes from the cryo-TEM image reconstructions was revisited. (Top) As detailed in Materials and Methods, the program package SITUS was used to refit the structures in an unbiased manner. In the previous crystal structure (27), there are two conformations for the P domain that were designated subunits A (green) and B (brown). The heavy and light chains for the Fab are shown in red and blue, respectively. (Bottom) Details of the fitted ensemble. The two loops that comprise the epitope are splayed apart in the A conformation compared to the B conformation. This causes severe clashes in the case of the B conformation (left side) compared to the A conformation (right side). Furthermore, the splayed conformation of A exposes a hydrophobic patch that complements the similarly nonpolar CDR3 heavy-chain loop.