The 26S protease responsible for the selective degradation of ubiquitinated proteins is composed of a regulator complex and the 20S proteosome which is the catalytic core. In the absence of ATP the 26S protease dissociates to free regulator complex and 20S proteosome, and this process can be reversed in vitro in the presence of ATP. Trypsin, chymotrypsin or proteinase K digestion selectively removes several subunits of the free regulator complex of Drosophila 26S protease generating a well-defined new subparticle. Three subunits highly sensitive in the free regulator complex, however, were selectively protected within the in vitro reconstituted 26S protease, indicating that the ATP-dependent association of the 20S proteosome in the regulator complex selectively shields these subunits. In the same concentration range the 20S proteosome was completely resistant for proteolytic degradation.