The binding protein of the fourth component of complement (C4-BP) is a regulatory protein of the complement system with specific affinity for the fourth component. This paper describes a structural polymorphism ofmurine C4-BP and its linkage to the major histocompatibility complex of the mouse (H-2). After isoelectric focusing of whole mouse plasma in low-endosmosis agarose, C4-BP was demonstrated as a single precipitin band by overlaying monospecific antiserum on the agarose gel. Two C4-BP patterns were distinguished among many strains of mice on the basis of isoelectric point-C4-BP a type, which has a pH range of 6.5-7.0 (exemplified by B10.BR and B1O.AKM), and C4-BP b type, which has a pH range of 6.3-6.6 (exemplified by BlO and B1O.M) The major histocompatibility complex of higher vertebrates contains a remarkable cluster of genes that collectively control transplantation antigens, immune response, and biosynthesis of complement proteins. The complement system, one of the major defense mechanisms of vertebrates against microbial organisms, consists of perhaps 20 component proteins (e.g., C2, C3, C4) (1). Complement proteins can be activated by two pathways, the classical and the alternative. By either pathway, a unique enzyme complex (C3 convertase) is assembled. C3 convertase consists of either C2 and C4 (the classical pathway C3 convertase) or factor B and C3 (the alternative pathway C3 convertase) and plays a key role in the amplification process ofcomplement activation (1). Studies from many laboratories, including ours, have demonstrated the linkages between the major histocompatibility complex and the loci controlling biosynthesis of these constituents of C3 convertase. Thus, the linkages to major histocompatibility complex of the genes controlling the following traits has been established: (i) serum C4 (Ss protein) level in mouse (2, 3); (ii) allotypic difference of C4 in mouse (4-6), guinea pig (7), and man (8-10); (iii) deficiency ofC4 in man (11) and guinea pig (12); (iv) expression of a subclass of mouse C4 (sex-limited protein) (13); (v) allotype (14, 15) and deficiency (16) ofhuman C2; (vi) serum C2 level in mouse (17); (vii) allotype of factor B in man (18-21), rhesus monkey (22), and guinea pig (12); and (viii) allotype of mouse C3 (23-26). It should be emphasized that, of the many complement proteins, none but these constituent proteins of the amplification C3 convertase are under the genetic control of major histocompatibility complex-linked loci (27-29).We report here that murine C4-binding protein (C4-BP), a recently isolated complement protein that has regulatory functions for the C3 convertase of the classical pathway, is also controlled by a major histocompatibility complex-linked locus.C4-BP is a macromolecular serum protein that has an electrophoretic mobility of (3-globulin. It was first isolated from mouse plasma on the basis ofits unique molecular structure and strong affinity for the activated form of C4 (Ss) proitin (30).Then, a homologous protein was purified to homogen...