Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Ancient evolutionary origin of diversified variable regions demonstrated by crystal structures of an immune-type receptor in amphioxus

Nature Immunology volume 7, pages 875–882 (2006)Cite this article

Abstract

Although the origins of genes encoding the rearranging binding receptors remain obscure, it is predicted that their ancestral forms were nonrearranging immunoglobulin-type domains. Variable region–containing chitin-binding proteins (VCBPs) are diversified immune-type molecules found in amphioxus (Branchiostoma floridae), an invertebrate that diverged early in deuterostome phylogeny. To study the potential evolutionary relationships between VCBPs and vertebrate adaptive immune receptors, we solved the structures of both a single V-type domain (to 1.15 Å) and a pair of V-type domains (to 1.85 Å) from VCBP3. The deduced structures show integral features of the ancestral variable-region fold as well as unique features of variable-region pairing in molecules that may reflect characteristics of ancestral forms of diversified immune receptors found in modern-day vertebrates.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Get just this article for as long as you need it

$39.95

Learn more

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Structural comparison of the VCBP3 domain fold and packing interactions with antigen receptors.
Figure 2: Noncanonical interactions in the core of VCBP3 V1 solved by multiple-wavelength anomalous dispersion and refined to 1.15 Å.
Figure 3: Packing interactions in antigen receptors and paired V-type immunoglobulin domains in VCBP3.
Figure 4: Structural elements at the V-domain interface.
Figure 5: Crystal structure of VCBP3 V1·V2 solved by single-wavelength anomalous dispersion and refined to 1.85 Å.
Figure 6: The distribution of known binding sites in V domains occupying alternative surfaces in the V-type fold in the TCR, a V-type viral receptor and the contiguous region of hypervariation in VCBPs.

Accession codes

Accessions

GenBank/EMBL/DDBJ

Protein Data Bank

References

  1. Orengo, C.A. & Thornton, J.M. Protein families and their evolution—a structural perspective. Annu. Rev. Biochem. 74, 867–900 (2005).

    Article  CAS  Google Scholar 

  2. Bork, P., Holm, L. & Sander, C. The immunoglobulin fold. Structural classification, sequence patterns and common core. J. Mol. Biol. 242, 309–320 (1994).

    CAS  Google Scholar 

  3. Barclay, A.N. Membrane proteins with immunoglobulin-like domains–a master superfamily of interaction molecules. Semin. Immunol. 15, 215–223 (2003).

    Article  CAS  Google Scholar 

  4. Hunkapiller, T. & Hood, L. Diversity of the immunoglobulin gene superfamily. Adv. Immunol. 44, 1–62 (1989).

    Article  CAS  Google Scholar 

  5. Eason, D.D. et al. Mechanisms of antigen receptor evolution. Semin. Immunol. 16, 215–226 (2004).

    Article  CAS  Google Scholar 

  6. Chothia, C., Gelfand, I. & Kister, A. Structural determinants in the sequences of immunoglobulin variable domains. J. Mol. Biol. 278, 457–479 (1998).

    Article  CAS  Google Scholar 

  7. Garrett, T.P., Wang, J., Yan, Y., Liu, J. & Harrison, S.C. Refinement and analysis of the structure of the first two domains of human CD4. J. Mol. Biol. 234, 763–778 (1993).

    Article  CAS  Google Scholar 

  8. Leahy, D.J., Axel, R. & Hendrickson, W.A. Crystal structure of a soluble form of the human T cell coreceptor CD8 at 2.6 Å resolution. Cell 68, 1145–1162 (1992).

    Article  CAS  Google Scholar 

  9. Cantoni, C. et al. The three-dimensional structure of the human NK cell receptor NKp44, a triggering partner in natural cytotoxicity. Structure (Camb.) 11, 725–734 (2003).

    Article  CAS  Google Scholar 

  10. Laird, D.J., De Tomaso, A.W., Cooper, M.D. & Weissman, I.L. 50 million years of chordate evolution: seeking the origins of adaptive immunity. Proc. Natl. Acad. Sci. USA 97, 6924–6926 (2000).

    Article  CAS  Google Scholar 

  11. Litman, G.W., Cannon, J.P. & Dishaw, L.J. Reconstructing immune phylogeny: new perspectives. Nat. Rev. Immunol. 5, 866–879 (2005).

    Article  CAS  Google Scholar 

  12. Desmyter, A. et al. Crystal structure of a camel single-domain VH antibody fragment in complex with lysozyme. Nat. Struct. Biol. 3, 803–811 (1996).

    Article  CAS  Google Scholar 

  13. Stanfield, R.L., Dooley, H., Flajnik, M.F. & Wilson, I.A. Crystal structure of a shark single-domain antibody V region in complex with lysozyme. Science 305, 1770–1773 (2004).

    Article  CAS  Google Scholar 

  14. Garcia, K.C. et al. Structural basis of plasticity in T cell receptor recognition of a self peptide-MHC antigen. Science 279, 1166–1172 (1998).

    Article  CAS  Google Scholar 

  15. Cannon, J.P., Haire, R.N. & Litman, G.W. Identification of diversified genes that contain immunoglobulin-like variable regions in a protochordate. Nat. Immunol. 3, 1200–1207 (2002).

    Article  CAS  Google Scholar 

  16. Cannon, J.P., Haire, R.N., Schnitker, N., Mueller, M.G. & Litman, G.W. Individual protochordates possess unique immune-type receptor repertoires. Curr. Biol. 14, R465–R466 (2004).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  18. Medzhitov, R. & Janeway, C.A., Jr Advances in immunology: innate immunity. N. Engl. J. Med. 343, 338–344 (2000).

    Article  CAS  Google Scholar 

  19. Zhang, S-M., Adema, C.M., Kepler, T.B. & Loker, E.S. Diversification of Ig superfamily genes in an invertebrate. Science 305, 251–254 (2004).

    Article  CAS  Google Scholar 

  20. Watson, F.L. et al. Extensive diversity of Ig-superfamily proteins in the immune system of insects. Science 309, 1874–1878 (2005).

    Article  CAS  Google Scholar 

  21. Wang, J.W. et al. SAD phasing by combination of direct methods with the SOLVE/RESOLVE procedure. Acta Crystallogr. D Biol. Crystallogr. 60, 1244–1253 (2004).

    Article  CAS  Google Scholar 

  22. Schneider, T.R. & Sheldrick, G.M. Substructure solution with SHELXD. Acta Crystallogr. D Biol. Crystallogr. 58, 1772–1779 (2002).

    Article  Google Scholar 

  23. Carter, P., Andersen, C.A. & Rost, B. DSSPcont: Continuous secondary structure assignments for proteins. Nucl. Acids Res. 31, 3293–3295 (2003).

    Article  CAS  Google Scholar 

  24. Holm, L. & Sander, C. Protein folds and families: sequence and structure alignments. Nucl. Acids Res. 27, 244–247 (1999).

    Article  CAS  Google Scholar 

  25. Dauter, Z., Lamzin, V.S. & Wilson, K.S. The benefits of atomic resolution. Curr. Opin. Struct. Biol. 7, 681–688 (1997).

    Article  CAS  Google Scholar 

  26. Babu, M.M. NCI: A server to identify non-canonical interactions in protein structures. Nucl. Acids Res. 31, 3345–3348 (2003).

    Article  CAS  Google Scholar 

  27. Kolodny, R., Koehl, P. & Levitt, M. Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. J. Mol. Biol. 346, 1173–1188 (2005).

    Article  CAS  Google Scholar 

  28. Li, H. et al. Structure of the Vδ domain of a human γδ T-cell antigen receptor. Nature 391, 502–506 (1998).

    Article  CAS  Google Scholar 

  29. Clements, C.S. et al. The crystal structure of myelin oligodendrocyte glycoprotein, a key autoantigen in multiple sclerosis. Proc. Natl. Acad. Sci. USA 100, 11059–11064 (2003).

    Article  CAS  Google Scholar 

  30. van Raaij, M.J., Chouin, E., van der Zandt, H., Bergelson, J.M. & Cusack, S. Dimeric structure of the coxsackievirus and adenovirus receptor D1 domain at 1.7 Å resolution. Structure 8, 1147–1155 (2000).

    Article  CAS  Google Scholar 

  31. Ostrov, D.A., Shi, W., Schwartz, J.C., Almo, S.C. & Nathenson, S.G. Structure of murine CTLA-4 and its role in modulating T cell responsiveness. Science 290, 816–819 (2000).

    Article  CAS  Google Scholar 

  32. Kaufman, J. The origins of the adaptive immune system: whatever next? Nat. Immunol. 3, 1124–1125 (2002).

    Article  CAS  Google Scholar 

  33. Rudolph, M.G., Luz, J.G. & Wilson, I.A. Structural and thermodynamic correlates of T cell signaling. Annu. Rev. Biophys. Biomol. Struct. 31, 121–149 (2002).

    Article  CAS  Google Scholar 

  34. Luz, J.G. et al. Structural comparison of allogeneic and syngeneic T cell receptor-peptide-major histocompatibility complex complexes: a buried alloreactive mutation subtly alters peptide presentation substantially increasing V(β) Interactions. J. Exp. Med. 195, 1175–1186 (2002).

    Article  CAS  Google Scholar 

  35. Lo Conte, L., Chothia, C. & Janin, J. The atomic structure of protein-protein recognition sites. J. Mol. Biol. 285, 2177–2198 (1999).

    Article  Google Scholar 

  36. Suzuki, T., Shin, I., Fujiyama, A., Kohara, Y. & Kasahara, M. Hagfish leukocytes express a paired receptor family with a variable domain resembling those of antigen receptors. J. Immunol. 174, 2885–2891 (2005).

    Article  CAS  Google Scholar 

  37. Haruta, C., Suzuki, T. & Kasahara, M. Variable domains in hagfish: NICIR is a polymorphic multigene family expressed preferentially in leukocytes and is related to lamprey TCR-like. Immunogenetics 58, 216–225 (2006).

    Article  CAS  Google Scholar 

  38. Seeger, M.A. & Kaufman, T.C. Characterization of amalgam: a member of the immunoglobulin superfamily from Drosophila. Cell 55, 589–600 (1988).

    Article  CAS  Google Scholar 

  39. Streltsov, V.A. et al. Structural evidence for evolution of shark Ig new antigen receptor variable domain antibodies from a cell-surface receptor. Proc. Nat. Acad. Sci. USA 101, 12444–12449 (2004).

    Article  CAS  Google Scholar 

  40. Cannon, J.P., Haire, R.N., Rast, J.P. & Litman, G.W. The phylogenetic origins of the antigen binding receptors and somatic diversification mechanisms. Immunol. Rev. 200, 12–22 (2004).

    Article  CAS  Google Scholar 

  41. Raskin, D.M., Seshadri, R., Pukatzki, S.U. & Mekalanos, J.J. Bacterial genomics and pathogen evolution. Cell 124, 703–714 (2006).

    Article  CAS  Google Scholar 

  42. Chatterji, M., Tsai, C.L. & Schatz, D.G. New concepts in the regulation of an ancient reaction: transposition by RAG1/RAG2. Immunol. Rev. 200, 261–271 (2004).

    Article  CAS  Google Scholar 

  43. Fugmann, S.D., Messier, C., Novack, L.A., Cameron, R.A. & Rast, J.P. An ancient evolutionary origin of the Rag1/2 gene locus. Proc. Natl. Acad. Sci. USA 103, 3728–3733 (2006).

    Article  CAS  Google Scholar 

  44. Delsuc, F., Brinkmann, H., Chourrout, D. & Philippe, H. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 439, 965–968 (2006).

    Article  CAS  Google Scholar 

  45. Hernandez Prada, J.A., Haire, R.N., Cannon, J.P., Litman, G.W. & Ostrov, D.A. Crystallization and preliminary x-ray analysis of VCBP3 from Branchiostoma floridae. Acta Crystallogr. D Biol. Crystallogr. 60, 2022–2024 (2004).

    Article  Google Scholar 

  46. Weeks, C.M. et al. Automatic solution of heavy-atom substructures. Methods Enzymol. 374, 37–83 (2003).

    Article  CAS  Google Scholar 

  47. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).

    Article  CAS  Google Scholar 

  48. Kantardjieff, K.A. & Rupp, B. Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals. Protein Sci. 12, 1865–1871 (2003).

    Article  CAS  Google Scholar 

  49. Terwilliger, T.C. & Berendzen, J. Automated MAD and MIR structure solution. Acta Crystallogr. D Biol. Crystallogr. 55, 849–861 (1999).

    Article  CAS  Google Scholar 

  50. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A. 47, 110–119 (1991).

    Article  Google Scholar 

  51. Brunger, A.T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54, 905–921 (1998).

    Article  CAS  Google Scholar 

  52. Laskowski, R.A., Moss, D.S. & Thornton, J.M. Main-chain bond lengths and bond angles in protein structures. J. Mol. Biol. 231, 1049–1067 (1993).

    Article  CAS  Google Scholar 

  53. McRee, D.E. XtalView/Xfit–A versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125, 156–165 (1999).

    Article  CAS  Google Scholar 

  54. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).

    Article  Google Scholar 

  55. Lefranc, M.P. et al. IMGT-ONTOLOGY for immunogenetics and immunoinformatics. In Silico Biol. 4, 17–29 (2004).

    CAS  Google Scholar 

Download references

Acknowledgements

We thank B. Pryor for editorial assistance. Supported by the National Institutes of Health (R01 AI23338 to G.W.L. and R01 DE013883 and R21 HL080222 to D.A.O.), the Cure Autism Now Foundation (2908051-12 to D.A.O.), the US Department of Energy (DE-AC02-98CH10886 for beamline X6A) and the National Institutes of Health, National Institute of General Medical Sciences (GM-0080 for beamline X6A).

Author information

Authors and Affiliations

  1. Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, 32610, Florida, USA

    José A Hernández Prada & David A Ostrov

  2. Department of Pediatrics, University of South Florida College of Medicine, Children's Research Institute, St. Petersburg, 33701, Florida, USA

    Robert N Haire, John P Cannon & Gary W Litman

  3. Brookhaven National Laboratory National Synchroton Light Source, Upton, 11973, NY, USA

    Marc Allaire, Jean Jakoncic & Vivian Stojanoff

  4. Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, 33612, Florida, USA

    John P Cannon & Gary W Litman

  5. Department of Molecular Genetics, All Children's Hospital, St. Petersburg, 33701, Florida, USA

    Gary W Litman

Authors
  1. José A Hernández Prada
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Robert N Haire
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Marc Allaire
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jean Jakoncic
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Vivian Stojanoff
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. John P Cannon
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Gary W Litman
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. David A Ostrov
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

J.A.H.P., crystallization, data collection, data reduction, structure determination, structural refinement, structural analysis and composition of the manuscript; R.N.H., protein expression, refolding and purification of recombinant V1 and V1-V2 VCBPs and contributions to the manuscript; M.A., space-group determination and phase determination and cryoprotection of native and selenomethionine crystals for the high-resolution structure of VCBP3 V1 (1XT5); J.J., data collection, space-group determination and phase determination of native and selenomethionine crystals of VCBP3 V1V2 (2FBO); V.S., data collection supervision and mounting of native and selenomethionine crystals of VCBP3 V1(1XT5) and V1V2 (2FBO); J.P.C., generation of constructs for VCBP3 V1 and VCBP3 V1V2 expression and contributions to the manuscript; G.W.L., data analysis, interpretation, discussions and fundamental contributions to the manuscript; D.A.O., crystal mounting, cryoprotection, supervision of MAD and native data collection of VCBP3 V1 and SAD and native collection of VCBP3 V1V2 (2FBO) and fundamental contributions to the manuscript.

Corresponding authors

Correspondence to Gary W Litman or David A Ostrov.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Table 1

Data collection and reduction statistics for VCBP3 crystals. (PDF 65 kb)

Supplementary Table 2

Refinement statistics for VCBP3 crystal structures. (PDF 60 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Prada, J., Haire, R., Allaire, M. et al. Ancient evolutionary origin of diversified variable regions demonstrated by crystal structures of an immune-type receptor in amphioxus. Nat Immunol 7, 875–882 (2006). https://doi.org/10.1038/ni1359

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ni1359

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing