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Structural basis of semaphorin–plexin signalling

Abstract

Cell-cell signalling of semaphorin ligands through interaction with plexin receptors is important for the homeostasis and morphogenesis of many tissues and is widely studied for its role in neural connectivity, cancer, cell migration and immune responses1. SEMA4D and Sema6A exemplify two diverse vertebrate, membrane-spanning semaphorin classes (4 and 6) that are capable of direct signalling through members of the two largest plexin classes, B and A, respectively2,3. In the absence of any structural information on the plexin ectodomain or its interaction with semaphorins the extracellular specificity and mechanism controlling plexin signalling has remained unresolved. Here we present crystal structures of cognate complexes of the semaphorin-binding regions of plexins B1 and A2 with semaphorin ectodomains (human PLXNB11–2–SEMA4Decto and murine PlxnA21–4–Sema6Aecto), plus unliganded structures of PlxnA21–4 and Sema6Aecto. These structures, together with biophysical and cellular assays of wild-type and mutant proteins, reveal that semaphorin dimers independently bind two plexin molecules and that signalling is critically dependent on the avidity of the resulting bivalent 2:2 complex (monomeric semaphorin binds plexin but fails to trigger signalling). In combination, our data favour a cell-cell signalling mechanism involving semaphorin-stabilized plexin dimerization, possibly followed by clustering, which is consistent with previous functional data. Furthermore, the shared generic architecture of the complexes, formed through conserved contacts of the amino-terminal seven-bladed β-propeller (sema) domains of both semaphorin and plexin, suggests that a common mode of interaction triggers all semaphorin–plexin based signalling, while distinct insertions within or between blades of the sema domains determine binding specificity.

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Figure 1: The semaphorin–plexin complexes share a common architecture.
Figure 2: Similar characteristics mediate the semaphorin–plexin interactions.
Figure 3: Bivalent interaction is critical for semaphorin–plexin-induced cell-cell signalling.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Coordinates and structure factors for PLXNB11–2–SEMA4Decto, PlxnA21–4–Sema6Aecto, Sema6Aecto and PlxnA21–4 have been deposited in the Protein Data Bank with succession numbers 3OL2, 3OKY, 3OKW and 3OKT, respectively.

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Acknowledgements

We thank the staff of European Synchrotron Radiation Facility beamline ID 23-1 and Diamond beamline I03 for assistance with data collection, the Molecular Cytogenetics and Microscopy Core facility of the Wellcome Trust Centre for Human Genetics, T. S. Walter for help with crystallization, G. Sutton for help with MALS experiments, A.F. Sonnen for help with AUC experiments, W. Lu for help with tissue culture, J. M. Grimes for assistance with figures and A. R. Aricescu and D. I. Stuart for critical reading of the manuscript. This work was funded by Cancer Research UK and the UK Medical Research Council. B.J.C.J. is funded by the Human Frontier Science Program, K.J.M. by a Science Foundation Ireland grant, C.H.B. and C.S. by the Wellcome Trust and E.Y.J. by Cancer Research UK.

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All authors contributed to the design of the project, data analysis and preparation of the manuscript. R.A.R. cloned, purified and performed SPR and MALS experiments on SEMA4D and PLXNB1 and crystallized and solved its complex structure. C.S. helped with the PLNXB1–SEMA4D complex structure solution. B.J.C.J. cloned, purified and performed SPR, AUC and MALS experiments on Sema6A and PlxnA2 and crystallized and solved the individual and complex structures. C.H.B. did the collapse assays, purified and performed AUC experiments on PLXNB1cyto and helped with other AUC experiments. F.P.-B. performed the granule cell migration assays.

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Correspondence to E. Yvonne Jones.

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The authors declare no competing financial interests.

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Janssen, B., Robinson, R., Pérez-Brangulí, F. et al. Structural basis of semaphorin–plexin signalling. Nature 467, 1118–1122 (2010). https://doi.org/10.1038/nature09468

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