The mechanism of chain selection and trimerization of fibrilassociated collagens with interrupted triple helices (FACITs) differs from that of fibrillar collagens that have special C-propeptides. We recently showed that the second carboxylterminal non-collagenous domain (NC2) of homotrimeric collagen XIX forms a stable trimer and substantially stabilizes a collagen triple helix attached to either end. We then hypothesized a general trimerizing role for the NC2 domain in other FACITs. Here we analyzed the NC2 domain of human heterotrimeric collagen IX, the only member of FACITs with all three chains encoded by distinct genes. Upon oxidative folding of equimolar amounts of the ␣1, ␣2, and ␣3 chains of NC2, a stable heterotrimer with a disulfide bridge between ␣1 and ␣3 chains is formed. Our experiments show that this heterotrimerization domain can stabilize a short triple helix attached at the carboxylterminal end and allows for the proper oxidation of the cystine knot of type III collagen after the short triple helix.The fibril-associated collagens with interrupted triple helices (FACITs) 2 include types IX, XII, XIV, XVI, XIX, XX, XXI, and XXII. Collagen IX is a heterotrimer composed of three distinct ␣ chains, and all others are homotrimers whose ␣ chains are characterized by short collagenous domains (COL) interrupted by several non-collagenous domains (NC) (1, 2). Unlike the fibril-forming collagens, the FACITs have significantly shorter NC1 domains (the carboxyl-terminal NC domains) (75 residues for human collagen XII, fewer than 30 residues for human collagen IX, and even fewer than 20 residues for human collagen XIX), whereas those of fibrillar collagens are of a different type and comprise about 260 residues. The FACITs share a remarkable sequence homology at their COL1/NC1 junctions by having two strictly conserved cysteine residues separated by four residues in the NC1 domain. These cysteines form interchain disulfide bonds, a so-called cystine knot, but only after the triple helix is formed (3-6). In other words, the NC1 domain cannot trimerize itself and requires exogenous alignment of three chains. It has been suggested that the NC2 domain in all FACITs is able to form an ␣-helical coiled coil, thus bearing an ability to trimerize those collagens (7). Experimental evidence for that was recently reported by us for the NC2 domain of collagen XIX (6).Collagen IX contains three collagenous domains (COL1-COL3) and four noncollagenous domains (NC1-NC4) (Fig. 1). The molecule is covalently associated with the surface of interstitial collagen fibrils in cartilage (8), where it plays a role in maintaining the long term structural integrity of this tissue (9). Loss of collagen IX is associated with such diseases as osteoarthritis, rheumatoid arthritis, intervertebrate disk degeneration, ocular defects, loss of hearing, and others (9 -13).Collagen IX is the most intriguing FACIT collagen in terms of its chain selection and heterotrimerization properties. Several attempts were made to decipher its code. Reasso...