The S region of the murine major histocompatibility complex controls the expression of two related, serum substance-positive proteins; one (C4) has functional complement activity, whereas the other, the sex-limited protein (Slp), is hemolytically nonfunctional. The whether the Slp-positive and Slp-negative subclasses of Ss protein represent the products of two distinct but closely linked and highly homologous structural genes in the S region, or whether the gene controlling the Slp variant might act via modification of the product of the Ss structural gene.Major progress in characterization of the Ss protein was made when it was demonstrated that it is antigenically (3, 4), structurally (3, 4), and functionally (5) homologous to the fourth component of human complement (C4). These observations were extended by studies in this laboratory (6) and subsequently by others (7), showing that the molecular weights of the isolated a-, p3-, and y-chains of the Ss protein (approximately 100,000, 75,000, and 34,000, respectively) are very similar to those reported for humans (8) and guinea pigs (9) C4. Differences were demonstrated in the apparent molecular weights of both the a-and y-chains between the Slp-negative and Slp-positive subclasses of Ss (6, 7). It was therefore proposed (6) that the Slp-positive and Slp-negative Ss molecules have different primary structures and represent the products of two discrete genes.Roos et al. (6) found an intracellular molecule with an apparent molecular weight of 185,000 which reacted with anti-Ss antibody-a putative C4 precursor. In accord with an earlier finding by Hall and Colten (10), in which an apparent singlechain precursor for guinea pig C4 was synthesized in a cell-free translation system, these findings suggested that a single structural gene might determine all three subunits of the C4 molecule.Recent data have also shown functional differences between Slp-positive and Slp-negative Ss molecules. Ferreira et al. (7) showed that the action of complement component C1 on Slp-negative molecules resulted in the cleavage of a small fragment (presumably C4a) from the a-chain, whereas no effect of complement component C1 on Slp-positive molecules was noted. Furthermore, functional studies with a hemolytic assay employing C4-deficient guinea pig serum indicated that only the Slp-negative Ss molecules possess C4 activity (ref. 7; J. P. Atkinson and D. C. Shreffler, unpublished results).The goals of the present study were 2-fold. First, we sought to demonstrate conclusively a precursor-product relationship between the 185,000-dalton intracellular molecules and the processed Slp-positive and Slp-negative Ss molecules. To this end, a combination of kinetic pulse-chase studies and structural comparisons by tryptic peptide mapping has been performed which confirms the suggestion (6) that the putative precursors give rise to the processed extracellular molecules. Second, the structural differences between Slp-positive and Slp-negative Ss molecules were further examined. Evidence ...