Goodpasture's (GP) disease is caused by autoantibodies that target the ␣3(IV) collagen chain in the glomerular basement membrane (GBM). Goodpasture autoantibodies bind two conformational epitopes (E A and E B ) located within the non-collagenous (NC1) domain of this chain, which are sequestered within the NC1 hexamer of the type IV collagen network containing the ␣3(IV), ␣4(IV), and ␣5(IV) chains. In this study, the quaternary organization of these chains and the molecular basis for the sequestration of the epitopes were investigated. This was accomplished by physicochemical and immunochemical characterization of the NC1 hexamers using chain-specific antibodies. The hexamers were found to have a molecular composition of (␣3) 2 (␣4) 2 (␣5) 2 and to contain cross-linked ␣3-␣5 heterodimers and ␣4-␣4 homodimers. Together with association studies of individual NC1 domains, these findings indicate that the ␣3, ␣4, and ␣5 chains occur together in the same triple-helical protomer. In the GBM, this protomer dimerizes through NC1-NC1 domain interactions such that the ␣3, ␣4, and ␣5 chains of one protomer connect with the ␣5, ␣4, and ␣3 chains of the opposite protomer, respectively. The immunodominant Goodpasture autoepitope, located within the E A region, is sequestered within the ␣3␣4␣5 protomer near the triple-helical junction, at the interface between the ␣3NC1 and ␣5NC1 domains, whereas the E B epitope is sequestered at the interface between the ␣3NC1 and ␣4NC1 domains. The results also reveal the network distribution of the six chains of collagen IV in the renal glomerulus and provide a molecular explanation for the absence of the ␣3, ␣4, ␣5, and ␣6 chains in Alport syndrome.