Extended Data Fig. 5: Generation of the apoB100 model and its orientation to the cholesteryl ester plates.
From: Structure of apolipoprotein B100 bound to the low-density lipoprotein receptor
a–d, AlphaFold generates low-confidence initial models relative to the built model of apoB100 (blue), LDLR (pink), and legobody (grey). Five AlphaFold2 structure predictions (pipe-and-plank diagrams coloured orange to green by confidence) for residues 1770–2801, α2 and nearby β-belt (a,b) and residues 3370–4563, α3 and nearby β-belt (c,d) of apoB100. a,c, One AlphaFold model (orange/green) and the final model of apoB100 (blue), LDLR (pink), and legobody (grey/tan) superpositioned and docked into density (yellow surface). Incompletely filled densities for α2 and α3 are labelled. The unfilled densities are predicted as pairs of helices, but this secondary structure is unresolved. Five superpositioned AlphaFold models of α2 and nearby belt (b) and α3 and nearby belt (d) in two, opposing views. e, Relative orientation of protein and cholesteryl ester plates. Two opposing views of the licorice diagram of apoB100, LDLR, and legobody (coloured as in Fig. 3) in the 1:2:1 complex density (light grey surface, 0.075 threshold) wrapping diagonally around three cholesteryl ester (CE) plates (solid surfaces) proximal to α2 (yellow), middle (pink), and proximal to α3 (cyan). α2 and α3 skirt the edges of their adjacent CE plates as labelled with the α-solenoid spanning all three CE plates.
