Abstract
Phosphoinositide-3 kinase (PI3K) is a central regulator of cellular metabolism and survival, and its dysregulation is implicated in major human diseases, particularly cancer. The p85 regulatory subunit of PI3K uses its C-terminal domains to stabilise the catalytic p110 subunit in an inhibited state. Certain Src homology 3 (SH3) domains activate p110 by binding to the proline-rich (PR) 1 motif at the N-terminus of p85. How this interaction leads to PI3K activation remains unclear. Moreover, the low specificity of SH3 domains raises the question about how they can selectively control PI3K activation. Combining structural, biophysical, and functional methods, we demonstrate that both questions are linked: PI3K-activating SH3 domains form additional ‘tertiary’ interactions with the C-terminal domains of p85, relieving p110 inhibition. SH3 domains lacking these tertiary contacts may bind p85 with similar affinity but fail to activate PI3K. Thus, p85 employs a selection mechanism that discriminates based on binding mode rather than binding strength, preventing nonspecific activation rather than nonspecific binding. This mechanism conveys a functional selectivity to SH3 domains that are otherwise considered promiscuous. These insights establish a mechanistic framework that will help to predict, modulate, and therapeutically target SH3-driven PI3K activation in disease.
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All data generated or analysed during this study are included in this published article and its supplementary information files. The source data underlying graphs, plots and charts in the manuscript are presented in Supplementary Data 2. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD058464.
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Acknowledgements
The research reported in this publication was supported by King Abdullah University of Science and Technology (KAUST) through the baseline fund to S.T.A. and M.J. J.E.L. acknowledges support from the Cancer Research UK Grant C57233/A22356. L.W.C. was supported by the Hong Kong Research Grants Council (17122021, 17104022), and J.W.B. was supported by NCI 1P01CA257885. We acknowledge SOLEIL for provision of synchrotron radiation facilities and would like to thank P. Legrand, S. Sirigu, M. Savko and B. Shepard for assistance in using the beamlines PROXIMA 1 and PROXIMA 2 A (on crystalline material from p85 fragments), and Aurelien Thureau and Javier Perez for assistance using the beamline SWING. For computer time, this research used the resources of the KAUST Supercomputing Laboratory, and experimental research was supported by the Bioscience Core Lab, ACL Proteomics Lab and the Imaging and Characterisation Core Lab at King Abdullah University of Science & Technology (KAUST) in Thuwal, Saudi Arabia.
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Conception of the project: S.T.A. Recombinant protein production: S.S.A., A.A., A.S., S.A., A.A.M., A.L., S.T.A.; Experimental data acquisition and analysis for ITC: S.S.A., A.A., A.S., A.A.M., S.A., S.T.A., J.E.L.; Experimental data acquisition and analysis for NMR: S.S.A., A.L., A.S., S.A., U.S., A.A.M., X.M., Ł.J., M.J., M.N.; XLMS: A.S., A.A.M.; DSF: A.S., A.A.; SAXS: A.S.; Activity assays: H.W., J.B., P.W., V.C.Y.M., L.W.T.C. AlphaFold modelling and analysis: S.T.A.; Contributed reagents, instrument time and lab facilities: J.B., Ł.J., M.J., S.T.A., J.B., X.M., L.W.T.C. Supervision: S.T.A., J.B., L.W.T.C., J.E.L., Ł.J., M.J., M.N., A.A.M., A.S., X.M. Writing of the initial manuscript: S.T.A. All authors read and commented on the manuscript.
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Aljedani, S.S., Sandholu, A., Aldehaiman, A. et al. SH3 domains selectively activate the PI3 kinase through non-conventional tertiary contacts. Commun Biol (2026). https://doi.org/10.1038/s42003-026-09540-y
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DOI: https://doi.org/10.1038/s42003-026-09540-y
