The complement system is a key component of innate and adaptive immune responses. Complement regulation is critical for prevention and control of disease. We have determined the crystal structure of the complement regulatory enzyme human factor I (fI). FI is in a proteolytically inactive form, demonstrating that it circulates in a zymogen-like state despite being fully processed to the mature sequence. Mapping of functional data from mutants of fI onto the structure suggests that this inactive form is maintained by the noncatalytic heavy-chain allosterically modulating activity of the light chain. Once the ternary complex of fI, a cofactor and a substrate is formed, the allosteric inhibition is released, and fI is oriented for cleavage. In addition to explaining how circulating fI is limited to cleaving only C3b/C4b, our model explains the molecular basis of disease-associated polymorphisms in fI and its cofactors. T he complement system is a major component of innate and adaptive immunity whose efficient regulation is critical for prevention and control of disease (1). This regulation is effected by host cells expressing and recruiting a series of proteins that protect them from complement-mediated destruction. A key step in this self-protection is the proteolytic cleavage of complement C3b (and its homolog C4b) by the serine protease complement factor I (fI) (2) in the presence of additional regulatory proteins termed "cofactors" (3). In the absence of regulation by fI the alternative pathway of complement leads to continuous generation of fluid-phase and cell-surface-deposited C3b by a self-amplification loop: The more C3 is converted to C3b, the more C3 convertases are formed, resulting in the depletion of C3 (4). With healthy levels of functional fI and its cofactors, the irreversible breakdown of C3b to iC3b has three effects: (i) arrest of the assembly of the C3 convertases on hostcell surfaces, thus avoiding inappropriate complement amplification; (ii) prevention of runaway C3 consumption in the fluid phase; and (iii) generation of the C3b cleavage fragments that go on to bind specific complement receptors and are involved in opsonization and triggering of the adaptive immune response (5). The importance of this regulatory mechanism is highlighted by the fact that fI-deficient individuals suffer from recurring infections and that polymorphisms in or near the genes for fI (and its cofactors) can predispose the carriers to diseases such as systemic lupus erythematosus, atypical hemolytic-uremic syndrome (aHUS), membranoproliferative glomerulonephritis, and age-related macular degeneration (for a recent review, see ref. 6).During the last few years, biochemical and structural data for complement regulators and C3/C3b in complex with regulators and inhibitors (7-11) have significantly advanced our understanding of the molecular mechanisms underlying complement regulation (12). To date, however, only low-resolution information about fI has been available (13, 14). FI is synthesized as a single 66-kDa chain an...