Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity

Clustered protocadherin (Pcdh) proteins mediate dendritic self-avoidance in neurons via specific homophilic interactions in their extracellular cadherin (EC) domains. We determined crystal structures of EC1–EC3, containing the homophilic specificity-determining region, of two mouse clustered Pcdh isoforms (PcdhγA1 and PcdhγC3) to investigate the nature of the homophilic interaction. Within the crystal lattices, we observe antiparallel interfaces consistent with a role in trans cell-cell contact. Antiparallel dimerization is supported by evolutionary correlations. Two interfaces, located primarily on EC2-EC3, involve distinctive clustered Pcdh structure and sequence motifs, lack predicted glycosylation sites, and contain residues highly conserved in orthologs but not paralogs, pointing toward their biological significance as homophilic interaction interfaces. These two interfaces are similar yet distinct, reflecting a possible difference in interaction architecture between clustered Pcdh subfamilies. These structures initiate a molecular understanding of clustered Pcdh assemblies that are required to produce functional neuronal networks. [Display omitted] •Clustered protocadherin EC1–3 fragments form antiparallel complexes in crystals•A full extracellular cadherin repeat region model yields an extended molecule•Isoform-specific conservation of interfaces explains strict homophilic specificity•Evolutionary correlations provide support for antiparallel arrangement Nicoludis et al. determined the structures of two clustered protocadherin fragments and found they formed antiparallel complexes. The authors provide a scaffold for isoform-specific interfaces and propose a full-length antiparallel complex that is responsible for homophilic trans interactions that mediate self-avoidance during synaptogenesis.