A ternary Neurexin-T178-PTPR complex represents a core-module of neuronal synapse organization

The organization of cell-cell contacts is fundamental for multi-cellular life and operation of organs. Synapses, prototypic contact sites for neuronal communication, are key to brain function and work over the last decades identified multiple synaptic cell adhesion molecules (sCAMs) that drive their organization. Whether these sCAMs operate independently or in coordination through yet unknown linker proteins remained elusive. Here, we used a systematic large-scale multi-epitope affinity-purification approach combined with quantitative mass spectrometry and immuno-EM to comprehensively map trans-synaptic protein networks in the mouse brain. We discover a presynaptic core-module assembled from the two major sCAM families, Neurexins1-3 and LAR-type receptor protein tyrosine phosphatases (PTPRD,S,F), and the previously uncharacterized tetraspanin proteins T178A, B. These ternary Neurexin-T178-PTPR complexes form through their trans-membrane domains and assemble during biogenesis in the ER. Loss of T178B results in module dissociation, strong reduction of LAR-PTPRs and re-distribution of synaptic Neurexins. At synapses, the Neurexin-T178-PTPR module recruits stable and extended trans-synaptic protein networks with defined pre- and post-synaptic partners and secreted extracellular linkers. The network architecture robustly interlinks the distinct functional modules/machineries of the presynaptic active zone and establishes tight associations with XKR-type lipid scramblases and postsynaptic GABAergic and glutamatergic neurotransmitter receptors. Our data identify a universal presynaptic core-module for synaptic adhesion and trans-synaptic signaling in the mammalian brain.