Fig. 2: Crystal structure of Affilin Af2 in complex with the target 7B8. | Communications Biology

Fig. 2: Crystal structure of Affilin Af2 in complex with the target 7B8.

From: Ubiquitin-derived artificial binding proteins targeting oncofetal fibronectin reveal scaffold plasticity by β-strand slippage

Fig. 2

a The crystal structure of Affilin Af2 bound to oncofetal Fn fragment 7B8 revealing three target-binding regions (I-III, dotted red elipsoids) involving the Fn domains EDB and Fn8. The β5-strands of Af2 Ubi-N (darker blue) and Ubi-C (darker red) exhibit distinct negative register shifts, remodelling the α2β5 loops involved in binding (coloured in cyan and magenta, respectively). Detailed view of key interactions between (b) Ub-N and EDB (interface I), (c) Ub-C and EDB (interface II) and (d) Ub-C and Fn8 (interface III). Residues involved in binding shown as sticks, other evolved amino acids as lines, hydrogen bonds depicted as yellow dashed lines, water molecules as red spheres. Residue colouring of C-atoms in cyan/light blue (Ub-N), magenta/light red (Ub-C), orange/blue (EDB). Ub-C residue numbers labelled with asterisk correspond to the residue numbering of the Ub-N domain.

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