Fig. 2. Structure of the complex between antibody 7D10 and BAK^L100A.

a The BAK^L100A moieties of the complex have elevated B-factors. The crystallographic asymmetric unit contains four BAK polypeptides (central) with four attached Fv fragments. Colouring is by B factor (low-blue, high-red) indicating that the BAK parts of the image are more disordered. b In the crystal, BAK^L100A is an α3α4 domain-swapped dimer. Chain R of the BAK dimer is coloured rainbow (blue - α1 through red - α7), and chain P in white. In the left panel the pseudo dyad symmetry axis is vertical. The cross-over connections between α4 and α5 are at the top of the figure. The cross-over connections between α2 and α3 are in the centre of the figure where the symmetry breaks down. This connection is built for the chain R (cyan - α2 to green - α3), but no interpretable electron density is observed for α3 on the chain P (white dashed lines). The epitope segments are at the bottom of the figure, the dashed lines indicating disorder in those parts of the α1-α2 loop C-terminal to the epitope. In the right panel the view is down the pseudo dyad symmetry axis. The cross-over connections between α4 and α5 are in the foreground near the symmetry axis. c The α3α4 domain-swapped BAK^L100A dimer binds two copies of the 7D10 Fv fragment. The BAK^L100A moieties occlude each other in this view. Chain R of the BAK dimer (coloured rainbow) engages Light chain Variable domain (light pink) and Heavy chain Variable domain (dark pink) in the foreground, with chain R (white) to Light chain Variable domain (light grey) and Heavy chain Variable domain (dark grey) at the rear. The crystal asymmetric unit contains two essentially identical copies of this dimer. d The BAK epitope snakes its way across a binding crevice in the 7D10 Fv (pink surface). BAK residues shown as sticks are ⁴⁸EAEGVAAPADPEM⁶⁰ with contacting residues in bold in the sequence. Side chains of E48, E59 and M60 are disordered and shown as alanine.