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Structural basis of Dscam isoform specificity

Abstract

The Dscam gene gives rise to thousands of diverse cell surface receptors1 thought to provide homophilic and heterophilic recognition specificity for neuronal wiring2,3,4 and immune responses5. Mutually exclusive splicing allows for the generation of sequence variability in three immunoglobulin ecto-domains, D2, D3 and D7. We report X-ray structures of the amino-terminal four immunoglobulin domains (D1–D4) of two distinct Dscam isoforms. The structures reveal a horseshoe configuration, with variable residues of D2 and D3 constituting two independent surface epitopes on either side of the receptor. Both isoforms engage in homo-dimerization coupling variable domain D2 with D2, and D3 with D3. These interactions involve symmetric, antiparallel pairing of identical peptide segments from epitope I that are unique to each isoform. Structure-guided mutagenesis and swapping of peptide segments confirm that epitope I, but not epitope II, confers homophilic binding specificity of full-length Dscam receptors. Phylogenetic analysis shows strong selection of matching peptide sequences only for epitope I. We propose that peptide complementarity of variable residues in epitope I of Dscam is essential for homophilic binding specificity.

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Figure 1: Structure of the N-terminal four-domain fragment of Dscam.
Figure 2: Homophilic dimers observed in the crystal lattice.
Figure 3: Epitope I confers homophilic binding specificity.
Figure 4: Phylogenetic comparison reveals differential sequence conservation of epitopes I and II.

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Acknowledgements

We thank K. Tan for discussion, and E. Reinherz, M. Eck and B. Chen for comments on the manuscript. We also thank R. Zhang and A. Joachimiak at the 19ID beamline of the Advanced Photon Source at the Argonne National Laboratory, and A. Soares at the X25 beamline at the Brookhaven National Synchrotron Light Source for help in X-ray data collection. The molecular electron microscopy facility at Harvard Medical School was established by a generous donation from the Giovanni Armenise Harvard Center for Structural Biology and is maintained by an NIH grant to T.W. We are grateful to S. L. Zipursky and W. Wojtowicz for discussions and the sharing of unpublished results. This work was supported by NIH grants to J.-h.W., D.S. and T.W., and a Pew Scholar Award and John Merck Fund Award to D.S. G.S. is a Damon Runyon fellow, supported by the Damon Runyon Cancer Research Foundation.

Atomic coordinates and structure factors have been deposited in the Protein Data Bank: 2V5M (Dscam D1–D41.34, space group P4222), 2V5S (Dscam D1–D41.34, space group C2221) and 2V5R (Dscam D1–D49.9, space group C2).

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Correspondence to Jia-huai Wang or Dietmar Schmucker.

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Meijers, R., Puettmann-Holgado, R., Skiniotis, G. et al. Structural basis of Dscam isoform specificity. Nature 449, 487–491 (2007). https://doi.org/10.1038/nature06147

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