Figure 1.

3D cryo-EM reconstruction of AAV-DJ complexed with SOS at 4.8 Å resolution. A: Peaks (segmented in red) are seen at the SOS binding sites in the map of the complex on the side of each spike that surrounds each viral 3-fold axis. B: The Δρ difference map (complex – native), contoured at 6σ shows, the SOS sulfate locations clearly, even at this resolution. Three of the sulfates appear to form salt bridge interactions with Arg₅₈₇ and Arg₅₉₀ from one of the exterior loops of the virus structure. C: Schematic of the central part of panel A showing the binding sites on three adjacent spikes related by icosahedral symmetry. As indicated by the two-tone arrows emanating from each SOS and pointing towards the 3-fold axis (triangle), a disaccharide could be bound at each site in the same orientation with respect to the local virus environment. The 8 Å resolution structure of the AAV-2 heparin complex (O'Donnell et al., 2009) shows diffuse density bridging between adjacent sites, consistent with a single polysaccharide passing through both sites. In such a case, the direction of the polysaccharide backbone in one site, relative to the local protein environment, would be the opposite of the direction at the adjacent site. This suggests that a virus that had evolved for polyvalent binding would have local binding sites tolerant of two GAG orientations.