Structure of the AAV-2 subunit and comparison with related structures. (a) Experimental electron density for AAV-2. Phases for this 3-Å resolution electron density map are independent of the AAV-2 model, having been obtained by symmetry averaging and extension from a CPV model at 15-Å resolution. Density is clear and allows an unambiguous fitting of the chemical sequence throughout VP3. (b) Ribbon drawing of the AAV-2 subunit. The locations of the neighboring symmetry axes are shown. The β-barrel is on the inner surface of the capsid (pink) with strands of the two sheets labeled conventionally as A, B, I, D, and G, and C, H, E, and F. Loops are labeled according to the flanking strands—e.g., GH loop. Regions where the sequence differs greatest between the AAV serotypes are colored purple (61). (c) Comparison of the backbones of AAV-2 (red) and canine parvovirus (cyan). The loop structure, which is responsible for many of the viral-host interactions differs substantially between AAV-2 and canine parvovirus, is largely absent from insect densoviruses (not shown).

Surface topology and electrostatics. (a–c) show grasp (67) surface renderings of AAV-2, canine parvovirus, and the insect densovirus, respectively, drawn to scale, and colored according to distance from the viral center. The view is down a twofold axis (center of the virus) with threefolds left and right of center, fivefolds above and below (see Fig. 4b). (d) shows the electrostatic surface potential of AAV-2 calculated with spock (68) running from −10 (red) to +10 (blue). The putative receptor-binding sites are positively charged patches on the side of each threefold-proximal peak, viewed edge-on (arrowed) or head-on where 3 equivalent patches join at each threefold (circled).

Conservation of sequence and secondary structure. Sequences of AAV-2 and CPV were aligned according to structure, then improved in loop regions according to sequence [Programs STAMP, PILEUP, and ALSCRIPT (62–66)]. Residues that are identical in AAV-2 and CPV are red. Those with an ALSCRIPT similarity score >5 (measured from 0 to 10) are yellow. Secondary structures of AAV-2 and CPV are compared, the core β-barrel highlighted in green, and labeled according to AAV-2 (CPV in parentheses where different). Side chain (outer) surface accessibility was calculated with a 1.5 Å radius probe, and is shown with triangles shaded according to each residue's accessibility: 20 Ų < red <50 Ų < cyan <80 Ų < green <100 Ų < blue.

Interdigitation of subunits: (a) shows a thin equatorial cross-section of AAV-2 (C_α traces) orthogonal to a twofold near the threefold axes. It emphasizes the elevation of the peaks, each of which comprises loops from two subunits that are colored differently. (b) a rhombic triacontahedron showing the viral orientation for Figs. 3 and 4. The three- and fivefold axes are at vertices joining three and five faces, respectively, and twofolds bisect neighboring threefolds, some of which are labeled. (Axes in parentheses superimpose, at an angle, upon twofolds behind.) The highlighted triangle (used in c) may be repeated sixtyfold with icosahedral symmetry operators to generate the entire capsid. (c) A schematic projection of one of the 60 triangular facets shows the surface amino acids with different subunits separated by purple lines. roadmap (69) was used to color as in a topographical map, with blue closest to the virus center, red farthest from the virus center. VP2 numbering is used with a letter prefix denoting the symmetry equivalent subunit.