Figure 2: Crystal structure of A3Fc-CD2.

(a) Ribbon diagram of A3Fc-CD2. The chain is coloured in a rainbow gradient from red (N terminus) to blue (C terminus). The catalytic zinc atom is labelled and shown as a grey sphere. The inset box shows a zoomed view of the catalytic site. (b) Structural difference between A3Fc-CD2, A3G-CD2 and A3C. All APOBEC3 cytosine deaminase domains have 10 loops. The largest structural deviations reside in loops L1, L2, L3, L4 and L7, coloured orange, green, red, blue and purple, respectively. (c) Multiple sequence alignment of A3F-CD2, A3C, A3D-CD2, A3G-CD1, A3G-CD2 and A3H. Numbering of the sequences and depiction of secondary structural elements are based on A3Fc-CD2, and is shown above the sequences. Strictly conserved residues are highlighted in red. Putative A3Fc-CD2 ssDNA-binding and Vif-binding residues are outlined in purple and blue boxes, respectively. Previously identified residues in the hydrophobic V-shaped groove formed by the α2 and α3 helices are outlined in yellow. Catalytic site residues are denoted with an asterisk above its sequence. The sequence alignment was produced using Clustal W^51,52 and the alignment graphics were generated using the programme ESPript⁵³.