One of two unstructured domains of Ii becomes ordered in complexes with MHC class II molecules.

We studied the role of the invariant chain (Ii) protein's structure in its ability to form complexes with major histocompatibility complex class II molecules. Multidimensional nuclear magnetic resonance experiments demonstrated that Ii contains two unstructured, flexible domains: a 39 residue sequence that contains a region (CLIP) critical for Ii/class II complex formation and becomes rapidly ordered when Ii/class II complexes are assembled, and a 30 residue sequence that contains the insertion point for a protease inhibitor domain included in an alternative splice form of Ii. Mobility of these domains guarantees accessibility to CLIP and the inhibitor insert, and ordering of the CLIP-containing domain may provide protection against proteolysis and contribute, along with Ii's compact 118-192 domain, to allotype-independent class II binding.