Cloning of the chicken alpha 3(IX) collagen chain completes the primary structure of type IX collagen.

Type IX collagen is composed of three genetically distinct polypeptides that contain several collagenous and non-collagenous domains. The alpha 2(IX) chain also contains a covalently bound glycosaminoglycan side chain. Type IX collagen is located on the surface of collagen fibrils of both hyaline cartilage and vitreous humor, such that one of the collagenous domains (COL3) projects from the surface of the fibril in a periodic manner. We have cloned and sequenced a full-length cDNA for the chicken alpha 3(IX) collagen chain from a cartilage cDNA library. Together with the sequence of the alpha 1(IX) and alpha 2(IX) chains, this completes the primary structure of type IX collagen for one species. These sequences will be useful to better understand the mechanism of triple-helix formation in type IX collagen and the nature of type II and type IX collagen interactions in fibril formation.