Within the MIIC, the Ii is removed from class II MHC molecules by the combined action of proteolytic enzymes and the HLA-DM molecule, and antigenic peptides are then able to bind to the available peptide-binding clefts of the class II molecules
Because the Ii blocks access to the peptide-binding cleft of a class II MHC molecule, it must be removed before complexes of peptide and class II molecules can form.
The same proteolytic enzymes, such as cathepsin S, that generate peptides from internalized proteins also act on the Ii, degrading it and leaving only a 24-amino acid remnant called class II–associated invariant chain peptide (CLIP).