Figure 3.

Comparison of A3G_NTD, A3C, A3D_CTD, A3F_CTD, and A3H hap II structures. (a) Cartoon and surface representations of the structure of A3G_NTD (PDB: 2MZZ), A3C (PDB: 3VOW), and A3D_CTD (a predicted model generated through homology modeling based on the A3F_CTD structure (PDB: 6NIL) by using the Phyre2 web portal for protein modeling, prediction and analysis [140], and A3H hap II (PDB: 6BBO). The known Vif-mediated degradation determinants labeled in red (for A3G and A3H), the critical residues for Vif-binding in magenta (for A3C, A3D, and A3F), and the CBFβ binding residues in cyan (for A3C, A3D, A3F). (b) Multiple sequence alignment of A3 domains (A3F_CTD, A3C, A3D_CTD) and the critical Vif- and CBFβ-binding residues are highlighted in yellow bars. A3F was used as a reference and hence the numbering is based on A3F’s residue numbers. The determinants for Vif- and CBFβ-binding are in non-overlapping regions, which are indicated above the alignment. (c,d) Similar primary sequences of residues in A3G_NTD and A3H hap II are shown, respectively. The residues highlighted in yellow bars are identified to be critical for Vif-mediated degradation of the respective A3 proteins. The sequence alignment was performed by a Clustal W multiple alignment in BioEdit.