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Targeting of a natural killer cell receptor family by a viral immunoevasin

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Abstract

Activating and inhibitory receptors on natural killer (NK) cells have a crucial role in innate immunity, although the basis of the engagement of activating NK cell receptors is unclear. The activating receptor Ly49H confers resistance to infection with murine cytomegalovirus by binding to the 'immunoevasin' m157. We found that m157 bound to the helical stalk of Ly49H, whereby two m157 monomers engaged the Ly49H dimer. The helical stalks of Ly49H lay centrally across the m157 platform, whereas its lectin domain was not required for recognition. Instead, m157 targeted an 'aromatic peg motif' present in stalks of both activating and inhibitory receptors of the Ly49 family, and substitution of this motif abrogated binding. Furthermore, ligation of m157 to Ly49H or Ly49C resulted in intracellular signaling. Accordingly, m157 has evolved to 'tackle the legs' of a family of NK cell receptors.

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Figure 1: Ly49-m157 interaction.
Figure 2: Docking of Ly49 on MHC class I and m157.
Figure 3: Structure of Ly49H NKD-α3s bound to m157.
Figure 4: Binding of mutant receptors of the Ly49 family to m157G1F.
Figure 5: Possible Ly49-MHC-m157 interactions at the cell surface.
Figure 6: Functional recognition of m157 by inhibitory and activating Ly49 receptors.

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References

  1. Davis, M.M. & Bjorkman, P.J. T-cell antigen receptor genes and T-cell recognition. Nature 334, 395–402 (1988).

    CAS  PubMed  Google Scholar 

  2. Tortorella, D., Gewurz, B.E., Furman, M.H., Schust, D.J. & Ploegh, H.L. Viral subversion of the immune system. Annu. Rev. Immunol. 18, 861–926 (2000).

    CAS  PubMed  Google Scholar 

  3. Yokoyama, W.M. & Plougastel, B.F. Immune functions encoded by the natural killer gene complex. Nat. Rev. Immunol. 3, 304–316 (2003).

    CAS  PubMed  Google Scholar 

  4. Natarajan, K., Dimasi, N., Wang, J., Mariuzza, R.A. & Margulies, D.H. Structure and function of natural killer cell receptors: multiple molecular solutions to self, nonself discrimination. Annu. Rev. Immunol. 20, 853–885 (2002).

    CAS  PubMed  Google Scholar 

  5. Smyth, M.J., Hayakawa, Y., Takeda, K. & Yagita, H. New aspects of natural-killer-cell surveillance and therapy of cancer. Nat. Rev. Cancer 2, 850–861 (2002).

    CAS  PubMed  Google Scholar 

  6. McQueen, K.L. & Parham, P. Variable receptors controlling activation and inhibition of NK cells. Curr. Opin. Immunol. 14, 615–621 (2002).

    CAS  PubMed  Google Scholar 

  7. Anderson, S.K., Ortaldo, J.R. & McVicar, D.W. The ever-expanding Ly49 gene family: repertoire and signaling. Immunol. Rev. 181, 79–89 (2001).

    CAS  PubMed  Google Scholar 

  8. Brown, M.G. et al. Vital involvement of a natural killer cell activation receptor in resistance to viral infection. Science 292, 934–937 (2001).

    CAS  PubMed  Google Scholar 

  9. Lee, S.H. et al. Susceptibility to mouse cytomegalovirus is associated with deletion of an activating natural killer cell receptor of the C-type lectin superfamily. Nat. Genet. 28, 42–45 (2001).

    CAS  PubMed  Google Scholar 

  10. Smith, H.R. et al. Recognition of a virus-encoded ligand by a natural killer cell activation receptor. Proc. Natl. Acad. Sci. USA 99, 8826–8831 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Rawlinson, W.D., Farrell, H.E. & Barrell, B.G. Analysis of the complete DNA sequence of murine cytomegalovirus. J. Virol. 70, 8833–8849 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Cosman, D. et al. A novel immunoglobulin superfamily receptor for cellular and viral MHC class I molecules. Immunity 7, 273–282 (1997).

    CAS  PubMed  Google Scholar 

  13. Adams, E.J. et al. Structural elucidation of the m157 mouse cytomegalovirus ligand for Ly49 natural killer cell receptors. Proc. Natl. Acad. Sci. USA 104, 10128–10133 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Corbett, A.J., Coudert, J.D., Forbes, C.A. & Scalzo, A.A. Functional consequences of natural sequence variation of murine cytomegalovirus m157 for Ly49 receptor specificity and NK cell activation. J. Immunol. 186, 1713–1722 (2011).

    CAS  PubMed  Google Scholar 

  15. Daniels, K.A. et al. Murine cytomegalovirus is regulated by a discrete subset of natural killer cells reactive with monoclonal antibody to Ly49H. J. Exp. Med. 194, 29–44 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Arase, H., Mocarski, E.S., Campbell, A.E., Hill, A.B. & Lanier, L.L. Direct recognition of cytomegalovirus by activating and inhibitory NK cell receptors. Science 296, 1323–1326 (2002).

    CAS  PubMed  Google Scholar 

  17. McWhorter, A.R. et al. Natural killer cell dependent within-host competition arises during multiple MCMV infection: consequences for viral transmission and evolution. PLoS Pathog. 9, e1003111 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Andrews, D.M. et al. Innate immunity defines the capacity of antiviral T cells to limit persistent infection. J. Exp. Med. 207, 1333–1343 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Long, E.O. Regulation of immune responses through inhibitory receptors. Annu. Rev. Immunol. 17, 875–904 (1999).

    CAS  PubMed  Google Scholar 

  20. Smith, K.M., Wu, J., Bakker, A.B., Phillips, J.H. & Lanier, L.L. Ly-49D and Ly-49H associate with mouse DAP12 and form activating receptors. J. Immunol. 161, 7–10 (1998).

    CAS  PubMed  Google Scholar 

  21. Back, J. et al. Distinct conformations of Ly49 natural killer cell receptors mediate MHC class I recognition in trans and cis. Immunity 31, 598–608 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Dam, J. et al. Variable MHC class I engagement by Ly49 natural killer cell receptors demonstrated by the crystal structure of Ly49C bound to H-2Kb. Nat. Immunol. 4, 1213–1222 (2003).

    CAS  PubMed  Google Scholar 

  23. Deng, L. et al. Molecular architecture of the major histocompatibility complex class I-binding site of Ly49 natural killer cell receptors. J. Biol. Chem. 283, 16840–16849 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Tormo, J., Natarajan, K., Margulies, D.H. & Mariuzza, R.A. Crystal structure of a lectin-like natural killer cell receptor bound to its MHC class I ligand. Nature 402, 623–631 (1999).

    CAS  PubMed  Google Scholar 

  25. Wang, J. et al. Binding of the natural killer cell inhibitory receptor Ly49A to its major histocompatibility complex class I ligand. Crucial contacts include both H-2Dd AND β2-microglobulin. J. Biol. Chem. 277, 1433–1442 (2002).

    CAS  PubMed  Google Scholar 

  26. Matsumoto, N., Mitsuki, M., Tajima, K., Yokoyama, W.M. & Yamamoto, K. The functional binding site for the C-type lectin–like natural killer cell receptor Ly49a spans three domains of its major histocompatibility complex class I ligand. J. Exp. Med. 193, 147–158 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Choi, T., Ferris, S.T., Matsumoto, N., Poursine-Laurent, J. & Yokoyama, W.M. Ly49-dependent NK cell licensing and effector inhibition involve the same interaction site on MHC ligands. J. Immunol. 186, 3911–3917 (2011).

    CAS  PubMed  Google Scholar 

  28. Brennan, J., Mahon, G., Mager, D.L., Jefferies, W.A. & Takei, F. Recognition of class I major histocompatibility complex molecules by Ly-49: specificities and domain interactions. J. Exp. Med. 183, 1553–1559 (1996).

    CAS  PubMed  Google Scholar 

  29. Voigt, V. et al. Murine cytomegalovirus m157 mutation and variation leads to immune evasion of natural killer cells. Proc. Natl. Acad. Sci. USA 100, 13483–13488 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Back, J., Chalifour, A., Scarpellino, L. & Held, W. Stable masking by H-2Dd cis ligand limits Ly49A relocalization to the site of NK cell/target cell contact. Proc. Natl. Acad. Sci. USA 104, 3978–3983 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Kielczewska, A., Kim, H.S., Lanier, L.L., Dimasi, N. & Vidal, S.M. Critical residues at the Ly49 natural killer receptor's homodimer interface determine functional recognition of m157, a mouse cytomegalovirus MHC class I-like protein. J. Immunol. 178, 369–377 (2007).

    CAS  PubMed  Google Scholar 

  32. Evans, E.J. et al. The T cell surface—how well do we know it? Immunity 19, 213–223 (2003).

    CAS  PubMed  Google Scholar 

  33. Xu, C., Call, M.E. & Wucherpfennig, K.W. A membrane-proximal tetracysteine motif contributes to assembly of CD3δɛ and CD3γɛ dimers with the T cell receptor. J. Biol. Chem. 281, 36977–36984 (2006).

    CAS  PubMed  Google Scholar 

  34. Moody, A.M. et al. Developmentally regulated glycosylation of the CD8αβ coreceptor stalk modulates ligand binding. Cell 107, 501–512 (2001).

    CAS  PubMed  Google Scholar 

  35. Hartmann, J. et al. The stalk domain and the glycosylation status of the activating natural killer cell receptor NKp30 are important for ligand binding. J. Biol. Chem. 287, 31527–31539 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Yoder, J. & Litman, G. The phylogenetic origins of natural killer receptors and recognition: relationships, possibilities, and realities. Immunogenetics 63, 123–141 (2011).

    CAS  PubMed  Google Scholar 

  37. Béziat, V. et al. NK cell responses to cytomegalovirus infection lead to stable imprints in the human KIR repertoire and involve activating KIRs. Blood 121, 2678–2688 (2013).

    PubMed  PubMed Central  Google Scholar 

  38. Gumá, M. et al. Imprint of human cytomegalovirus infection on the NK cell receptor repertoire. Blood 104, 3664–3671 (2004).

    PubMed  Google Scholar 

  39. Davis, A.H., Guseva, N.V., Ball, B.L. & Heusel, J.W. Characterization of murine cytomegalovirus m157 from infected cells and identification of critical residues mediating recognition by the NK cell receptor Ly49H. J. Immunol. 181, 265–275 (2008).

    CAS  PubMed  Google Scholar 

  40. French, A.R. et al. Escape of mutant double-stranded DNA virus from innate immune control. Immunity 20, 747–756 (2004).

    CAS  PubMed  Google Scholar 

  41. Clements, C.S., Kjer-Nielsen, L., Kostenko, L., McCluskey, J. & Rossjohn, J. The production, purification and crystallization of a soluble form of the nonclassical MHC HLA-G: the essential role of cobalt. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 62, 70–73 (2006).

    CAS  PubMed  Google Scholar 

  42. Aricescu, A.R., Lu, W. & Jones, E.Y. A time- and cost-efficient system for high-level protein production in mammalian cells. Acta Crystallogr. D Biol. Crystallogr. 62, 1243–1250 (2006).

    PubMed  Google Scholar 

  43. Schuck, P. Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling. Biophys. J. 78, 1606–1619 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Holst, J. et al. Generation of T-cell receptor retrogenic mice. Nat. Protoc. 1, 406–417 (2006).

    CAS  PubMed  Google Scholar 

  45. Sullivan, L.C. et al. The heterodimeric assembly of the CD94–NKG2 receptor family and implications for hman leukocyte antigen-E recognition. Immunity 27, 900–911 (2007).

    CAS  PubMed  Google Scholar 

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Acknowledgements

We thank the staff of the crystallization facility of Monash University for assistance; A. Shahine, R. Koh, M. Peverelli and I. Larma for technical assistance; S. Lemieux (Institut Armand-Frappier) for the 4LO3311 hybridoma; and W. Yokoyama (Washington University) for BWZ HD12 and BWZ DAP12 cells and the 3D10 hybridoma. This research was undertaken on the MX2 beamline at the Australian Synchrotron, Victoria, Australia. Supported by the National Health and Medical Research Council of Australia (M.J.C., R.B., L.C.S., J.D.C. and J.R.), Australian Research Council (M.A.P., M.J.C. and J.P.V.) and Pfizer Australia (T.B.).

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Contributions

R.B. solved the structure, undertook analysis, designed, did and interpreted experiments and contributed to the writing of the manuscript; N.N., P.M.S., J.P.V., J.L., F.A.D., A.J.C., C.A.F., J.M.W., L.C.S., A.D.M., M.A.P., M.J.C., A.A.S. and M.A.D.-E. provided reagents, did experiments and/or contributed to the writing of the manuscript; J.D.C. designed, undertook and analyzed the signaling experiments and contributed to the writing of the manuscript; and T.B., A.G.B. and J.R. contributed to the design and interpretation of experiments, project management and the writing of the manuscript.

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Correspondence to Travis Beddoe, Andrew G Brooks or Jamie Rossjohn.

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The authors declare no competing financial interests.

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Berry, R., Ng, N., Saunders, P. et al. Targeting of a natural killer cell receptor family by a viral immunoevasin. Nat Immunol 14, 699–705 (2013). https://doi.org/10.1038/ni.2605

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