A, crystal structure of human BCL-3 ankyrin repeat domain with β-hairpin (pink) and the inner and outer α helices (yellow) indicated. B, Bcl-3 binds specifically to GST-p50 in a GST pulldown assay. Purified bacterial recombinant GST or GST-p50 was incubated with a whole cell lysate from HEK293T cells transfected with empty vector (Mock) or FLAG-BCL-3 (BCL-3) and affinity purified with GSH-agarose. Pulldown complexes were immunoblotted with anti-FLAG and anti-GST antibodies. C, peptide arrays of immobilized overlapping 18-mer peptides, each shifted to the C terminus by 4 amino acids encompassing the entire BCL-3 sequence were generated. Arrays were probed with GST or GST-p50 and detected by immunoblotting with anti-GST antibody. Positive GST-p50 binding to BCL-3 peptides is shown (black spots) and is representative of duplicate arrays. Peptide identifier numbers are indicated. D, table of BCL-3 peptides 1–109 with corresponding BCL-3 amino acids and the structural region indicated. WB, Western blot.