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Here, we applied three-dimensional minimal flux optical nanoscopy to mouse IHC-SGN synapses to chart the positions of key pre- and postsynaptic proteins with single-digit nanometer resolution. We demonstrate that nanoclusters of ion channels and their interacting proteins govern the topography of AZs and postsynaptic densities (PSDs). We count synaptic proteins and their nanoclusters and determine their spatial organization, feeding into computational modeling of AZ function. 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