The monomeric form consists of two pseudosymmetrical eight-helix domains in which the helices are packed in a complex topology resembling that of the beta sheets in a jelly roll fold.

[1] The three-dimensional arrangement of helices forms a boat-shaped molecule with a large central cavity in which the pigments and lipids are bound.

[4][3] The most common 4:1 peridinin:chlorophyll ratio was predicted by spectroscopy in the 1970s,[5] but was unconfirmed until the crystal structure of the Amphidinium carterae PCP complex was solved in the 1990s.

[1] Whether formed from a protein monomer or dimer, the assembled protein-pigment complex is sometimes known as bPCP (for "building block") and is the minimal stable unit.

[4] In at least some PCP forms, including that from A. carterae, these building blocks assemble into a trimer thought to be the biologically functional state.