The molecular architecture of the desmosomal outer dense plaque by integrative structural modeling

Desmosomes are protein assemblies that mediate cell-cell adhesion and are prevalent in tissues under mechanical stress, such as heart and epithelial tissues. However, their detailed structural characterization is not yet available. Here, we characterized the molecular architecture of the desmosomal outer dense plaque (ODP) using Bayesian integrative structural modeling via IMP (Integrative Modeling Platform; https://integrativemodeling.org). We integrated information from X-ray crystallography, electron cryo-tomography, immuno-electron microscopy, yeast two-hybrid experiments, co-immunoprecipitation, in vitro overlay, in vivo co-localization assays, in-silico sequence-based predictions of transmembrane and disordered regions, homology modeling, and stereochemistry information to generate an integrative structure of the ODP. The structure was validated by additional information from biochemical assays that was not used in modeling. The ODP resembles a densely packed cylinder with two layers: a PKP layer and a PG layer; the desmosomal cadherins and PKP span the two layers. We identified previously unknown protein-protein interfaces between DP and Dsc, DP and PG, and PKP and the desmosomal cadherins. The integrative structure sheds light on the function of disordered regions, such as the N-terminus of PKP (N-PKP) and C-terminus of PG in desmosome assembly. In our structure, N-PKP interacts with several proteins in the PG layer, alluding to its importance in desmosome assembly, and implying that it is not merely a structural filler as previously posited. Further, we identified the structural basis for defective cell-cell adhesion in Naxos disease, Carvajal Syndrome, Skin Fragility/Woolly Hair Syndrome, and cancers via mapping of disease-related mutations on the structure. Finally, we point to features of the structure that could confer resilience to mechanical stress, such as the PG-DP interaction and the embedding of cadherins amidst the other proteins. Taken together, we contribute the most complete and robustly validated model of the desmosomal ODP so far, providing mechanistic insight into the function and assembly of desmosomes in normal and disease states.