Structures of neurexophilin–neurexin complexes reveal a regulatory mechanism of alternative splicing.

Neurexins are presynaptic, cell‐adhesion molecules that specify the functional properties of synapses via interactions with trans‐synaptic ligands. Neurexins are extensively alternatively spliced at six canonical sites that regulate multifarious ligand interactions, but the structural mechanisms underlying alternative splicing‐dependent neurexin regulation are largely unknown. Here, we determined high‐resolution structures of the complex of neurexophilin‐1 and the second laminin/neurexin/sex‐hormone‐binding globulin domain (LNS2) of neurexin‐1 and examined how alternative splicing at splice site #2 (SS2) regulates the complex. Our data reveal a unique, extensive, neurexophilin–neurexin binding interface that extends the jelly‐roll β‐sandwich of LNS2 of neurexin‐1 into neurexophilin‐1. The SS2A insert of LNS2 augments this interface, increasing the binding affinity of LNS2 for neurexophilin‐1. Taken together, our data reveal an unexpected architecture of neurexophilin–neurexin complexes that accounts for the modulation of binding by alternative splicing, which in turn regulates the competition of neurexophilin for neurexin binding with other ligands. Synopsis: Neurexins are presynaptic cell‐adhesion molecules that specify the functional properties of synapses via alternative splicing‐dependent interactions with various ligands. Our data reveal a unique interface architecture between the neurexin‐1 LNS2 domain and neurexophilin‐1 and show the mechanism of its regulation by alternative splicing. We determined high‐resolution crystal structures of two splice variants of the neurexin‐1 LNS2 domain in complex with neurexophilin.The LNS2‐neurexophilin‐1 complexes have a unique architecture wherein their individual beta‐sandwiches form one larger, contiguous beta‐sandwich.The architecture of the LNS2‐neurexophilin‐1 complex is regulated by alternative splicing.The neurexin SS2A insert in LNS2 augments the complex interface and increases the affinity of LNS2 for neurexophilin‐1. [ABSTRACT FROM AUTHOR]