Structure of the teneurin-latrophilin complex: Alternative splicing controls synapse specificity by a novel mechanism

The trans-synaptic interaction of the cell-adhesion molecules teneurins (Tenm’s) with latrophilins (Lphn’s) promotes excitatory synapse formation when Lphn’s simultaneously interact with FLRTs. Insertion of a short alternatively-spliced region within Tenm’s abolishes the Tenm-Lphn interaction and switches Tenm function to specify inhibitory synapses. How Tenm’s bind to Lphn’s in a manner regulated by alternative splicing remains unclear. Here, we report the high-resolution cryo-EM structure of the Tenm2-Lphn3 complex, and describe the trimeric Tenm2-Lphn3-FLRT3 complex. The structure reveals that the N-terminal lectin-like domain of Lphn3 binds to the Tenm2 barrel at a site far away from the alternatively-spliced region. Alternative-splicing regulates the Tenm2-Lphn3 interaction by hindering access to the Lphn-binding surface rather than altering it. Strikingly, mutagenesis of the Lphn-binding surface of Tenm2 abolishes the Lphn3 interaction and impairs excitatory but not inhibitory synapse formation. These results suggest that a multi-level coincident binding mechanism mediated by a cryptic adhesion complex between Tenm’s and Lphn’s regulates synapse specificity.