Collagens comprise a large superfamily of extracellular matrix proteins that play diverse roles in tissue function. The mechanism by which newly synthesized collagen chains recognize each other and assemble into specific triple-helical molecules is a fundamental question that remains unanswered. Emerging evidence suggests a role for the non-collagenous domain (NC1) located at the C-terminal end of each chain. In this study, we have investigated the molecular mechanism underlying chain selection in the assembly of collagen IV. Using surface plasmon resonance, we have determined the kinetics of interaction and assembly of the ␣1(IV) and ␣2(IV) NC1 domains. We show that the differential affinity of ␣2(IV) NC1 domain for dimer formation underlies the driving force in the mechanism of chain discrimination. Given its characteristic domain recognition and affinity for the ␣1(IV) NC1 domain, we conclude that the ␣2(IV) chain plays a regulatory role in directing chain composition in the assembly of (␣1) 2 ␣2 triple-helical molecule. Detailed crystal structure analysis of the [(␣1) 2 ␣2] 2 NC1 hexamer and sequence alignments of the NC1 domains of all six ␣-chains from mammalian species revealed the residues involved in the molecular recognition of NC1 domains. We further identified a hypervariable region of 15 residues and a -hairpin structural motif of 13 residues as two prominent regions that mediate chain selection in the assembly of collagen IV. To our knowledge, this report is the first to combine kinetics and structural data to describe molecular basis for chain selection in the assembly of a collagen molecule.Collagens comprise a major superfamily of extracellular matrix (ECM) 3 proteins that play a key role in the structural integrity of all tissues. At least 27 different collagen types, consisting of 42 distinct gene products, have been identified in vertebrates, underlining their vast diversity in biological functions such as tissue compartmentalization and specialization during the development (1). In the endoplasmic reticulum, the newly synthesized collagen chains assemble into triple-helical molecules with specific chain compositions, which oligomerize to form supramolecular structures, including filaments and networks after secretion to the ECM.Some collagens are obligate homotrimers, such as collagen III, which comprises three identical pro-␣1(III) chains forming an ␣1(III) 3 procollagen, whereas others form heterotrimers containing at least one different ␣-chain; such as collagen I (2). Despite significant sequence identity and a propensity to form triple helices, procollagen chains have an extraordinary ability to discriminate between each other in the endoplasmic reticulum to form specific collagen types. For example, skin fibroblasts express six highly homologous but genetically distinct fibrilforming procollagen chains that are assembled in a type-specific manner to form type I, III, and V collagens. The mechanism by which different collagen chains are selected for assembly is a fundamental question...