AAV2 crystal structure with superimposed AAV2-Hep minus AAV2 VLP positive difference map and heparin models. A) Shaded-surface electron density map of AAV2 (PDB accession No. 1LP3, ) (grey) with the positive density (red mesh, contoured at 1σ) close to the two-, three-, and fivefold axes, 2f pos, 3f pos and 5f pos1, respectively, superimposed. (B) Close-up of shaded-surface representation of VLP reconstruction (grey) and AAV2-Hep (pink, density not in present VLPs), with the pseudo-atomic coordinates of heparin oligosaccharides (solid red) modeled into positive density (red mesh). hep2f = decasaccahride (twofold symmetry related decasaccahride is also shown); hep3f = single disaccharide (threefold symmetry related models are also shown). (C) Ribbon diagram of an AAV2 VP3 trimer and modeled heparin molecules. Surface heparin binding residues, R484, K527, K532, R585, and R588, are shown in blue (Arginines) or light blue (lysines) with terminal amino groups depicted as black balls. Residues from a reference monomer are denoted with A after the residue number; B indicates a threefold related residue. Heparin models are as labeled in (B). (D) Close up of basic (blue), acidic (orange) residues flanking the heparin binding residues. Basic residues are colored as in (C) and carboxyl groups are white for acidic residues. The broken lines indicate potential ionic interactions. The location of the icosahedral symmetry axes are labeled with numbers in (A–C). (A) is viewed along a twofold axis, and B, C, and D along a threefold axis. The figure was generated using Chimera ().