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. 2005 Apr;79(8):5047–5058. doi: 10.1128/JVI.79.8.5047-5058.2005

FIG. 5.

FIG. 5.

Comparison of AAV2, AAV4, and AAV5. (A) Superimposition of coil representations of the VP3 monomers of AAV2 atomic model coordinates (in red) (68) and of AAV4 (in blue) and AAV5 (in dark green) (63) pseudoatomic models built into the cryo-EM density. Variable surface loop regions (adjusted and unmodified) are labeled I to IX as in Fig. 3. The insert shows a snapshot (from the program O [34]) of the position of the intervening icosahedral threefold related VP3 loop (in cyan) and variable region VI. The residues that form the basic cluster in AAV2 (R484, R487, K532, R585, and R588 [VP1 numbering]) utilized for heparin binding are shown as small red balls and are labeled. The first N-terminal residue modeled (215), the C-terminal residue 734, and β-strands B to I are also labeled. (B) Coil representations of a trimer of AAV2 VP3s (in red, magenta, and cyan), an AAV4 monomer (in blue), and an AAV5 monomer (in dark green), viewed down the icosahedral threefold (solid triangle) axes. The superimposed AAV2, AAV4, and AAV5 monomers are shown rotated ∼90° relative to the view in panel A. The AAV2 basic residues become clustered from the threefold related monomers and are shown in the respective colors of their monomers and outlined in dotted ovals indicated by arrows. The positions of the variable regions (labeled I to IX) are shown as black, dark gray, and gray balls in the red, cyan, and magenta AAV2 monomers, respectively. Panels A and B were generated with the program Bobscript (20). (C) Close-up of the icosahedral threefold (solid triangle) axes of the pifmaps of AAV2 (left), AAV4 (center), and AAV5 (right), showing the local differences in topology of their threefold mounds. The resolution for each map is given on the bottom right-hand side of each panel. Approximate locations for variable regions I to VI are shown on top of one AAV2 monomer and mound. Arrows on the AAV2 surface indicate the approximate locations of the basic residues (shown in A and B) utilized for heparin binding (38, 46). The approximate icosahedral two-, three-, and five-fold axes are indicated by the filled ovals, triangles, and pentagons, respectively, in panels A to C.