Presynaptic active zone scaffold proteins ELKS2 and RIM1 function as supramolecular block copolymers that undergo microphase separation to generate hexagonally ordered nanodot arrays with ~130 nm spacing, where stoichiometry-dependent phase transitions and client protein interactions (Liprin-α disrupting order, RIMBP2 compacting spacing) dynamically modulate nanostructure morphology to control neurotransmitter release efficacy.

Neurotransmitters are released at presynaptic active zones, where a conserved cytomatrix exhibits nanoscale order first visualized by electron microscopy over half a century ago. However, the physical principles underlying this architecture have remained unclear. Here we show that active zone scaffolds act as protein block copolymers, whose nanoscale microphase separation produces hexagonally packed nanodot arrays. Super-resolution imaging combined with block-copolymer theory identifies ELKS and RIM as the minimal pair sufficient to reproduce this ordered lattice, mediated by orthogonal interactions between ELKS coiled-coil domains and RIM intrinsically disordered regions. Additional active zone proteins, including RIMBP and Liprin-α, modulate lattice spacing and morphology in a stoichiometry-dependent manner, coupling nanoscale order to neurotransmission. More broadly, block-copolymer microphase separation emerges as a design principle for constructing functional nanostructures in living systems.