Decoding BBSome Architecture and Interactions Using AlphaFold3

The BBSome, a complex of 8 conserved Bardet-Biedl syndrome (BBS) proteins, is essential for various cellular processes including cilia, but its structural organization and protein interactions remain elusive. Using AlphaFold3, we generated a structural model that closely aligns with recent cryo-EM data with an a-carbon root mean square deviation of 1.203 Å. Analysis of interface residues using PyMol revealed key interaction sites among subunits identified BBS1 and BBS9 as central interaction hubs. Polar contact analysis supported these findings, with BBS2 and BBS7 showing the highest number of polar contacts, indicating a strong interaction. Notably, we show that the common BBS1M390R mutation disrupts BBSome structural stability. Additionally, BBS4 was predicted to form a stable complex with pericentriolar material 1 (PCM1), potentially affecting centriolar satellite localization. We further examined BBSome interactions with G protein-coupled receptors (GPCRs), identifying interaction hotspots on specific subunits, particularly BBS1 and BBS4, while BBS5 residues formed polar contacts with certain GPCRs. Interestingly, our analysis revealed that BBSome binding to BBS3 causes significant changes in BBSome-GPCR interaction, rather interaction with BBS1 or BBS5, the GPCRs interact with BBS2, BBS7 and BBS3. Furthermore, BBSome proteins directly interact with MRAP2, an accessory protein that mediate the cilia localization of the GPC, melanocortin-4 receptor. These interactions were validated through immunoprecipitation and functional peptide competition assays. Interestingly, AlphaFold3 predictions also revealed critical residues mediating interactions between BBS1 and the leptin receptor, and between BBS17 and the insulin receptor. Collectively, these findings advance our understanding of BBSome structural organization and function, establishing a predictive framework for investigating its role in ciliopathies and related human diseases. This abstract was presented at the American Physiology Summit 2026 and is only available in HTML format. There is no downloadable file or PDF version. The Physiology editorial board was not involved in the peer review process.