Significance We analyzed 46 molecular structures of the yeast proteasome core particle (CP) by principal component analysis (PCA) and discovered two distinct configurations of the principal proteolytic subunit β5: the apo-cluster encompassing complexes with nonpeptidic ligands and the pep-cluster of complexes with peptidic ligands. Both configurations differ by a small domain motion and numerous slight global changes, thus enabling intersubunit communication. PCA was expanded to the mouse CP and revealed a striking difference between the constitutive CP and the immune CP. The former conforms to the yeast system and executes the structural change seen in yeast, although both immune apo and liganded CP classify into the pep configuration, a possible explanation for the generally higher activity of the immune proteasome.