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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.

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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.

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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).

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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

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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.

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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)

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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

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