SummaryInvariant chain (Ii) contributes in a number of distinct ways to the proper functioning of major histocompatibility complex (MHC) class II molecules. These include promoting effective association and folding of newly synthesized MHC class II c~ and B subunits, increasing transit of assembled heterodimers out of the endoplasmic reticulum (ER), inhibiting class II peptide binding, and facilitating class II movement to or accumulation in endosomes/lysosomes. Although the cytoplasmic tail of Ii makes a key contribution to the endocytic localization of class II, the relationship between the structure of Ii and its other diverse functions remains unknown. We show here that two thirds of the lumenal segment of Ii can be eliminated without affecting its contributions to the secretory pathway events of class II folding, ElK to Golgi transport, or inhibition of peptide binding. These same experiments reveal that a short (25 residue) contiguous internal segment of Ii (the CLIP region), frequently found associated with purified MHC class II molecules, is critical for all three functions. Together with other recent findings, these results raise the possibility that the contributions of Ii to the early postsynthetic behavior of class II may depend on its interaction with the class II binding site. This would be consistent with the intracellular behavior of unoccupied MHC class I and class II molecules as incompletely folded proteins and imply a related structural basis for the similar contributions of Ii to class II and of short peptides to class I assembly and transport.U 'pon synthesis and translocation into the endoplasmic reticulum (ER) 1, the component chains of class I and class II MHC molecules need to acquire a transport-competent conformation for effective post-ER transport. To achieve proper folding and a stable heavy chain-B2 microglobulin interaction suitable for secretory pathway transit, MHC class I molecules require binding site occupancy with short peptides primarily generated in the cytosol and imported into the ER via TAP (1-3). In contrast, MHC class II molecules assemble as a stoichiometric complex with trimers of the type II integral membrane glycoprotein invariant chain (Ii) (4). In the secretory pathway, this association with Ii has effects on the properties of class II analogous to those resulting from peptide interaction with class I (3). Thus, interaction with intact Ii contributes to efficient, stable association of the class II c~ and j8 subunits in the ER (5, 6), promotes the transport of class II oe/~8 heterodimers from the ER through the Golgi complex (5, 7-10), and inhibits the binding of other ligands (peptides) to the class II molecules (11-13). Whether these multiple effects of Ii require the entire molecule or are medi1Abbreviations used in this paper: endo H, endoglycosidase H; ER, endoplasmic reticulum; Ii, invariant chain. ated by one or more structurally independent subregions of the protein is presently unknown. A particularly intriguing question is whether the effects of Ii on ...