A multitude of proteins in cells are assisted in their folding by double-ring chaperonin complexes. Chaperonin recognizes its substrates by its apical domain, which also interacts with cochaperonins. Here we describe the functional partitions of apical domains from two CPN60 subunit types. The apical domain of CPN60β1 could replace that of GroEL to complement GroEL function in E. coli. In contrast, the apical domain of CPN60α did not show functional replacement due to its inability to interact or cooperate with cochaperonin. Crystal structures of apical domains from CPN60β1 and CPN60α, solved at 1.5 ？ and 1.75 ？ respectively, revealed these rigid bodies merged well except for deviations in substrate binding sites, which may underlie the functional differences of these two subunit types. CPN60α binds to its cognate Rubisco large subunit more efficiently than CPN60β1, but does not functionally cooperate with cochaperonin like CPN60β1, because of two amino acids conserved among Cpn60α homologues (Q203, T241). The two types of Cpn60 subunits have functional divergency, but cooperate with each other to form functional oligomers. Our results strengthen substrates recognition specificity by individual chaperonin subunits and reveal their differenciate cooperation with cochaperonins for the first time.