Fig. 3.

Ubvs selected for binding to the F-box^Fbw7 or F-box^Fbw11 domain in complex with full-length Skp1. (A) Ubvs selected from Library 2 for binding to Skp1–F-box^Fbw7. Positions that were soft-randomized in the library are shown and residues conserved as Ubv.Fw7.1 sequence are indicated by dashes. Positions that diverge from the Ubv.Fw7.1 sequence but show consensus among the selected sequences are boxed and conserved residues at these positions are shaded gray. (B) Affinities of Ubv.Fw7.5, Ubv.Fw11.1, and Ubv.Fw11.2 for different Skp1–F-box complexes. “NB” indicates no detectable binding and “WB” indicates weak binding for which IC₅₀ values were >5,000 nM. Sequence of Ubv binding region (F-box residues located within 10 Å of Ubv in the structure of Skp1tr–F-box^Fbw7–Ubv.Fw7.1 complex) is shown for each F-box protein. Conserved positions are shaded gray and Fbw7 residues important for binding to Ubv.Fw7.1 (Fig. 2F) are boxed. (C) The sequences and affinities of Ubv.Fw11.1 and its derivatives selected for binding to Skp1–F-box^Fbw11. Only the sequence in region 1 that differs from Ubv.Fw7.5 is shown, and residues conserved as Ubv.Fw11.1 sequence are indicated by dashes.