Collagen IX, located on the surface of collagen fibrils, is crucial for cartilage integrity and stability. The N-terminal NC4 domain of the ␣1(IX) chain is probably important in this because it interacts with various macromolecules such as proteoglycans and cartilage oligomeric matrix protein. At least 17 distinct collagen polypeptides carry an NC4-like unit near their N terminus, but this report, describing the crystal structure of NC4 at 1.8-Å resolution, represents the first atomic level structure for these domains. The structure is similar to previously characterized laminin-neurexin-sex hormone binding globulin (LNS) structures, dominated by an antiparallel -sheet sandwich. In addition, a zinc ion was found in a position similar to that of the metal binding site of other LNS domains. A partial backbone NMR assignment of NC4 was obtained and utilized in NMR titration studies to investigate the zinc binding in solution state and to quantitate the affinity of metal binding. The K d of 11.5 mM suggests a regulatory rather than a structural role for zinc in solution. NMR titration with a heparin tetrasaccharide revealed the presence of a secondary binding site for heparin on NC4, showing structural and functional conservation with thrombospondin-1, but a markedly reduced affinity for the ligand. Also the overall arrangement of the N and C termini of NC4 resembles most closely the N-terminal domain of thrombospondin-1, distinguishing the two from the majority of the published LNS structures.Collagens are a family of extracellular matrix proteins comprised of at least 28 distinct types, all characterized by the presence of one or more elongated triple helical regions. This common motif is supplemented with a variety of non-helical domains to add unique properties for molecular or supramolecular assembly, for tissue-specific targeting, or for interactions with other constituents of the matrix (1, 2). An example of such a supplementary element is a module showing similarity to the N-terminal domains of thrombospondins (TSPNs) 2 (3). This domain occurs in at least 17 different collagen polypeptides, located N-terminal to the triple helix, but little is known about the detailed structures and physiological functions of these units (2).One of the TSPNs found in collagen chains is the NC4 domain of collagen IX, formed by about 245 N-terminal residues of the mature ␣1(IX) polypeptide. In cartilage tissue, collagen IX molecules are covalently bound to the heteropolymeric collagen fibrils that provide the tissue with high tensile strength to resist the swelling pressure caused by proteoglycans. The shorter arm of the triple helix of collagen IX projects away from the fibril body so that the NC4 domain can easily interact with other macromolecules. The temporal and spatial control over the presence or absence of NC4 on collagen IX via alternative splicing (4, 5) suggests that the domain has functional significance. The NC4 domain, as well as three other regions along the collagen IX triple helix, has been shown to interact...