Collagen XI is a heterotrimeric molecule found predominantly in heterotypic cartilage fibrils, where it is involved in the regulation of fibrillogenesis. This function is thought to involve the complex N-terminal domain. The goal of this current study was to examine its structural organization to further elucidate the regulatory mechanism. The amino-propeptide (␣1-Npp) alone or with isoforms of the variable region were recombinantly expressed and purified by affinity and molecular sieve chromatography. Cys-1-Cys-4 and Cys-2-Cys-3 disulfide bonds were detected by liquid chromatographytandem mass spectrometry. This pattern is identical to the homologous ␣2-Npp, indicating that the recombinant proteins were folded correctly. Anomalous elution on molecular sieve chromatography suggested that the variable region was extended, which was confirmed using rotary shadowing; the ␣1-Npp formed a globular "head" and the variable region an extended "tail." Circular dichroism spectra analysis determined that the ␣1-Npp comprised 33% -sheet, whereas the variable region largely comprised non-periodic structure. Taken together, these results imply that the ␣1-Npp cannot be accommodated within the core of the fibril and that the variable region and/or minor helix facilitates its exclusion to the fibril surface. This provides further support for regulation of fibril diameter by steric hindrance or by interactions with other matrix components that affect fibrillogenesis.Collagen XI is a component of fibrils both in cartilage and a wide variety of non-cartilaginous tissues, including brain, muscle, tendon, heart valve, skin, calvaria, and endochondral bone (1, 2). In cartilage it assembles with collagens II and IX to produce an extensive network of thin, heterotypic collagen fibrils (15-25 nm in diameter; Ref. 1) in which the other extracellular matrix components are embedded. The major triple helix of collagen XI is not accessible to antibodies unless the fibrils are disrupted, which led to the model that it is located in the interior of the fibril (1, 3). In non-cartilaginous tissues, collagen XI has been found to co-assemble with chains of the highly homologous type V collagen (4, 5).Collagen XI is a heterotrimeric molecule consisting of ␣1, ␣2, and ␣3 collagen chains (6). The ␣3(XI) chain is an overglycosylated form of the ␣1(II) collagen chain (7), whereas the ␣1(XI) and ␣2(XI) chains are distinct gene products (8). The ␣1(XI) and ␣2(XI) chains contain similar large, N-terminal domains (NTDs), 1 comprising a "PARP" or "PARP-like" domain, a variable region, and a minor triple helix ( Fig. 1a; Refs. 9 and 10). The PARP (proline-arginine rich protein) domain was originally isolated as a distinct protein from bovine cartilage (11) but was later demonstrated to be a fragment of the N terminus of the ␣2(XI) chain (12). Recently, the proteolytic processing site of the ␣1(XI) chain has been identified (13,14), and since nearly all of the domain is removed by this processing event, both the PARP-like and PARP domains are now termed the ...