An E beta DNA protein complex termed complex A, whose binding activity has recently been shown to correlate with both constitutive and regulated class II expression in murine cell lines, is also present in a human B cell, Raji. The DNA involved in complex A, which includes three previously defined transcriptional motifs, W, X, and Y, is a cis-acting transcription element in Raji cells. Both complex A binding activity and transcriptional activity of its target sequence are absent in an Ia- mutant subclone of Raji, RJ 2.2.5. This cell line, whose defect is complemented by a locus on mouse chromosome 16, reexpresses both class II and complex A upon transfection with mouse genomic DNA. We suggest that factors that form complex A or that regulate complex A formation account for the molecular lesion in this cell line.