Synaptic adhesion molecules orchestrate synaptogenesis. The presynaptic leukocyte
common antigen-related receptor protein tyrosine phosphatases (LAR-RPTPs) regulate
synapse development by interacting with postsynaptic Slit- and Trk-like family proteins
(Slitrks), which harbour two extracellular leucine-rich repeats (LRR1 and LRR2). Here we
identify the minimal regions of the LAR-RPTPs and Slitrks, LAR-RPTPs Ig1–3 and Slitrks LRR1,
for their interaction and synaptogenic function. Subsequent crystallographic and structureguided
functional analyses reveal that the splicing inserts in LAR-RPTPs are key molecular
determinants for Slitrk binding and synapse formation. Moreover, structural comparison of
the two Slitrk1 LRRs reveal that unique properties on the concave surface of Slitrk1 LRR1
render its specific binding to LAR-RPTPs. Finally, we demonstrate that lateral interactions
between adjacent trans-synaptic LAR-RPTPs/Slitrks complexes observed in crystal lattices
are critical for Slitrk1-induced lateral assembly and synaptogenic activity. Thus, we propose a
model in which Slitrks mediate synaptogenic functions through direct binding to LAR-RPTPs
and the subsequent lateral assembly of LAR-RPTPs/Slitrks complexes.