In animals, protease inhibitors of the serpin family are associated with many physiological processes, including blood coagulation and innate immunity. Serpins feature a reactive center loop (RCL), which displays a protease target sequence as a bait. RCL cleavage results in an irreversible, covalent serpin-protease complex. AtSerpin1 is an Arabidopsis protease inhibitor that is expressed ubiquitously throughout the plant. The x-ray crystal structure of recombinant AtSerpin1 in its native stressed conformation was determined at 2.2 Å . The electrostatic surface potential below the RCL was found to be highly positive, whereas the breach region critical for RCL insertion is an unusually open structure. AtSerpin1 accumulates in plants as a fulllength and a cleaved form. Fractionation of seedling extracts by nonreducing SDS-PAGE revealed the presence of an additional slower migrating complex that was absent when leaves were treated with the specific cysteine protease inhibitor L-trans-epoxysuccinyl-L-leucylamido (4-guanidino)butane. Significantly, RESPONSIVE TO DESICCATION-21 (RD21) was the major protease labeled with the L-trans-epoxysuccinyl-L-leucylamido (4-guanidino)butane derivative DCG-04 in wild type extracts but not in extracts of mutant plants constitutively overexpressing AtSerpin1, indicating competition. Fractionation by nonreducing SDS-PAGE followed by immunoblotting with RD21-specific antibody revealed that the protease accumulated both as a free enzyme and in a complex with AtSerpin1. Importantly, both RD21 and AtSerpin1 knock-out mutants lacked the serpin-protease complex. The results establish that the major Arabidopsis plant serpin interacts with RD21. This is the first report of the structure and in vivo interaction of a plant serpin with its target protease.Protease cascades are prominent mediators of rapid physiological responses in animals, playing a role in cellular immunity, blood clotting, and development. The proteolytic specificity of the serine and cysteine proteases involved dictates the fidelity of these reactions. The serpins are an important group of proteins that curb the activity of these cascades through specific irreversible inhibition of the proteases. For example, in Drosophila, the necrotic (nec) gene encodes a protease inhibitor of the serpin family. Necrotic protein controls a proteolytic cascade that activates the innate immune response to fungal and Gram-positive bacterial infections (1). In nec null mutants, Toll-mediated immune responses are constitutively activated, even in the absence of infection, implying that Nec continually restrains this immune response. As opposed to other types of protease inhibitors, serpins offer both an irreversible and tunable type of inhibition (reviewed in Ref.2). In their native conformation, serpins are in a stressed (spring-loaded) state with a solvent-exposed reactive center loop (RCL).3 Specific residues of the RCL are precisely accommodated by the target protease active site. Upon cleavage of the serpin peptide bond linking the P1 and ...