Both chains of HLA-DR bind to the membrane with a penultimate hydrophobic region and the heavy chain is phosphorylated at its hydrophilic carboxyl terminus.

The HLA-DR antigen, a complex of two glycoproteins of 29,000 and 34,000 daltons, can be isolated from the membranes of human B-lymphoblastoid cell lines. Extensive proteolysis releases only 5-10% of the antigen, whereas detergent solubilizes all of it. Detergent solubilization after papain proteolysis of membranes produces antigen with chains cleaved near the carboxyl termini. Comparison of these three preparations demonstrates that each chain contains a carboxyl-terminal hydrophilic region that is sensitive to proteolytic degradation and a penultimate hydrophobic region, responsible for membrane binding, that is more resistant to papain. This two-step cleavage of each chain is also observed during the proteolysis of detergent-solubilized HLA-DR antigen. Both chains of HLA-DR in the membrane can be labeled with the lipophilic photoactivatable carbene reagent adamantane diazirine. This label is released from both chains during the second cleavage. The heavy chain can be reduced and alkylated under mild conditions, and this label is also lost during the second cleavage. The heavy chain is phosphorylated in vivo, and this label is lost upon the first cleavage. This observation suggests that the carboxyl terminus of the heavy chain is intracellular. Cumulatively, these data suggest that both chains of HLA-DR antigens are comprised of large extracellular NH2-terminal regions, small penultimate intramembranous regions, and small carboxyl-terminal intracellular regions.