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A Collagen IV protomer is a three-chain molecular unit of Collagen IV that assembles with other units to form a basement membrane network. Much of its length has a collagen triple helix, while its C-terminus presents three Collagen IV NC1 domains. Association of two such ends forms a Collagen IV NC1 hexamer.^[ref]

The organizational levels can be counted separately. Ten intact three-chain Collagen IV protomers contain thirty polypeptide chains, but this count does not describe how the ten units are connected. A six-subunit NC1 junction joins two protomers at one end; it does not convert either protomer into a six-chain molecule.

The term is therefore useful when moving between a protein's molecular composition and the architecture of the scaffold it builds. Identifying a three-chain unit answers a different question from identifying the contacts and covalent bonds between neighbouring units.

G. Kartha worked with G. N. Ramachandran on the structure of collagen. Their 1955 paper developed a model in which three polypeptide chains wind around one another, contributing to the explanation of the collagen triple helix. The proposed arrangement had to accommodate the amino acid composition, hydrogen bonding and the pattern of experimental X-ray diffraction.^[ref]

The history illustrates how a structural model is tested. A geometrically plausible arrangement can still require revision if its predicted repeat disagrees with measured X-ray diffraction. The value of the model lies in connecting molecular packing with several independent observations, while leaving its detailed geometry open to correction. A proposed protein structure and a later experimentally refined atomic structure represent different stages of that process.^[ref]

J. Bella is the first author of a 1994 X-ray crystallography study of a collagen-like peptide. The structure, determined at 1.9 angstrom resolution, resolved a collagen triple helix and the surrounding water network. It connected the overall three-chain organization with individual hydrogen bonds and interactions involving hydroxyproline residues.^[ref]

The peptide contained a single glycine-to-alanine substitution. Near that position, the three-chain structure untwisted locally and water-mediated connections replaced some direct interchain hydrogen bonds. This gives a concrete example of how one change in protein primary structure can alter a local structural arrangement without erasing the whole fold. The observation concerns the studied peptide crystal; proposed parallels with mutant collagen in tissues are a further biological interpretation.^[ref]