The Antibody Combining Site

  • Edgar Haber
  • Jiří Novotný


Antibodies are characterized by regions of conserved as well as variable amino acid sequence. Small portions of each molecule, highly variable in structure (the complementarity-determining regions), are arranged to form the surface that binds antigen. The amino acid sequences of the polypeptide chain segments that fold to form this region (approximately 60 amino acid residues) determine the nature of the antigen recognized. Three segments of the heavy and three of the light chain participate in forming the site.


Light Chain Heavy Chain Partial Amino Acid Sequence Variable Region Gene Heavy Chain Variable Region 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Brack, C., Hirama, M., Lenhard-Schuller, R., and Tonegawa, S., 1978, A complete immunoglobulin gene is created by somatic recombination, Cell 15:1–14.PubMedCrossRefGoogle Scholar
  2. 2.
    Sakano, H., Kurosawa, Y., Weigert, M., and Tonegawa, S., 1981, Identification and nucleotide sequence of a diversity DNA segment (D) of immunoglobulin heavy-chain genes,Nature 290:562–565.PubMedCrossRefGoogle Scholar
  3. 3.
    Seidman, J. G., Leder, A., Nau, M., Norman, B., and Leder, P., 1978, Antibody diversity: The structure of cloned immunoglobulin genes suggests a mechanism for generating new sequences,Science 202:11–17.PubMedCrossRefGoogle Scholar
  4. 4.
    Seidman, J. G., Max, E. E., and Leder, P., 1979, A kappa-immunoglobulin gene is formed by site-specific recombination without further somatic mutation,Nature 280:370–375.PubMedCrossRefGoogle Scholar
  5. 5.
    Early, P., Huang, H., Davis, M., Calame, K., and Hood, L., 1980, An immunoglobulin heavy chain variable region gene is generated from three segments of DNA: VH, D, and JH, Cell 19:981–992.PubMedCrossRefGoogle Scholar
  6. 6.
    Weigert, M., Gatmaitan, L., Loh, E., Schilling, J., and Hood, L., 1978, Rearrangement of genetic information may produce immunoglobulin diversity,Nature 276:785–790.PubMedCrossRefGoogle Scholar
  7. 7.
    Tonegawa, S., 1983, Somatic generation of antibody diversity,Nature 302:575–581.PubMedCrossRefGoogle Scholar
  8. 8.
    Gearhart P. J., 1983, Effect of somatic mutation on antibody affinity, Ann. N.Y. Acad. Sci. 418:171–176.PubMedCrossRefGoogle Scholar
  9. 9.
    Clarke, S. H., Claflin, J. L., and Rudikoff, S., 1982, Polymorphisms in immunoglobulin heavy chains suggesting gene conversion, Proc. Natl. Acad. Sci. USA 79:3280–3284.PubMedCrossRefGoogle Scholar
  10. 10.
    Singer, S. J., and Doolittle R. F., 1966, Antibody active sites and immunoglobulin chains,Science 153:13–25.PubMedCrossRefGoogle Scholar
  11. 11.
    Hill, R. L., Delaney, R., Fellows, R. E., and Lebovitz, H. E., 1966, The evolutionary origins of the immunoglobulins, Proc.Natl. Acad. Sci. USA 56:1762–1769.PubMedCrossRefGoogle Scholar
  12. 12.
    Edelman, G. M., 1970, The covalent structure of a human gamma G-immunoglobulin. XI. Functional implications, Biochemistry 9:3197–3205.PubMedCrossRefGoogle Scholar
  13. 13.
    Hilschmann, N., and Craig, L. C., 1965, Amino acid sequence studies with Bence-Jones proteins, Proc. Natl. Acad. Sci. USA 53:1403–1409.PubMedCrossRefGoogle Scholar
  14. 14.
    Titani, K., Whitely, E., Avogardo, L., Putnam, F. M., 1965, Immunoglobulin structure: Partial amino acid sequence of a Bence-Jones protein,Science 149:1090–1092.PubMedCrossRefGoogle Scholar
  15. 15.
    Hochman, J., Inbar, D., and Givol, D., 1973, An active antibody fragment (Fv) composed of the variable portions of heavy and light chains, Biochemistry 12:1130–1135.PubMedCrossRefGoogle Scholar
  16. 16.
    Wu, T. T., and Kabat, E. A., 1970, An analysis of the sequences of the variable regions of Bence-Jones proteins and myeloma light chains and their implications for antibody complementarity, J. Exp. Med. 132:211–250.PubMedCrossRefGoogle Scholar
  17. 17.
    Marquart, M., Deisenhofer, J., Huber, R., and Palm, W., 1980, Crystallographic refinement and atomic models of the intact immunoglobulin molecule Kol and its antigen-binding fragment at 3.0 Å and 1.0 Å resolution, J. Mol. Biol. 141:369–391.PubMedCrossRefGoogle Scholar
  18. 18.
    Saul, F. A., Amzel, L. M., and Poljak, R. J., 1978, Preliminary refinement and structural analysis of the Fab fragment from human immunoglobulin new at 2.0 Â resolution, J. Biol. Chem. 253:585–595.PubMedGoogle Scholar
  19. 19.
    Segal, D. M., Padlan, E. A., Cohen, G. H., Rudikoff, S., Potter, M., and Davies, D. R., 1974, The three-dimensional structure of phosphorylcholine-binding mouse immunoglobulin Fab and theNatureof the antigen binding site, Proc. Natl. Acad. Sci. USA 71:4298–4302.PubMedCrossRefGoogle Scholar
  20. 20.
    Epp, O., Colman, P., Feilhammer, H., Bode, W., Schiffer, M., and Huber, R., 1974, Crystal and molecular structure of a dimer composed of the variable portions of the Bence-Jones protein REI, Eur. J. Biochem. 45:513–524.PubMedCrossRefGoogle Scholar
  21. 21.
    Schiffer, M., Girling, R. I., Ely, K. R., and Edmundson, A. B., 1973, Structure of a lambda-type Bence-Jones protein at 3.5-Å resolution, Biochemistry 12:1620–1631.CrossRefGoogle Scholar
  22. 22.
    Amzel, L. M., Poljak, R. J., Saul, F., Varga, J. M., and Richards, F. F., 1974, The three dimensional structure of a combining region-ligand complex immunoglobulin NEW at 3.5-Å resolution, Proc. Natl. Acad. Sci. USA 71:1427–1430.PubMedCrossRefGoogle Scholar
  23. 23.
    Richardson, J. S., 1981, The anatomy and taxonomy of protein structure, Adv. Protein Chem. 34:167–339.PubMedCrossRefGoogle Scholar
  24. 24.
    Lesk, M. A., and Chothia, C., 1982, Evolution of proteins formed by beta-sheets. II. The core of the immunoglobulin domains, J. Mol.Biol. 160:325–342.PubMedCrossRefGoogle Scholar
  25. 25.
    Edmundson, A. B., Ely, K. R., Abola, E. E., Schiffer, M., and Panagiotopoulos, N., 1975, Rotational allomerism and divergent evolution of domains in immunoglobulin light chains, Biochemistry 14:3953–3961.CrossRefGoogle Scholar
  26. 26.
    Pauling, L., and Corey, R. B., 1951, Configurations of polypeptide chains with favored orientations around single bonds: Two new pleated sheets, Proc. Natl. Acad. Sci. USA 37:729–740.PubMedCrossRefGoogle Scholar
  27. 27.
    Chothia, C., 1973, Conformation of twisted beta-pleated sheets in proteins, J. Mol. Biol. 75:295–302.PubMedCrossRefGoogle Scholar
  28. 28.
    Novotny, J., Bruccoleri, R., Newell, J., Murphy, D., Haber, E., and Karplus, M., 1983, Molecular anatomy of the antibody combining site, J. Biol. Chem. 258(23):14433–14437.PubMedGoogle Scholar
  29. 29.
    Bernard, O., and Gough, N. M., 1980, Nucleotide sequence of immunoglobulin heavy chain joining segments between translocated Vh and mu constant regions genes, Proc. Natl. Acad. Sci. USA 77:3630–3634.PubMedCrossRefGoogle Scholar
  30. 30.
    Newell, N., Richards, J. E., Tucker, P. W., and Blattner, F. R., 1980, J genes for heavy chain immunoglobulins of mouse,Science 209:1128–1132.PubMedCrossRefGoogle Scholar
  31. 31.
    Siebenlist, U., Ravetch J. V., Korsmeyer, S., Waldmann, T., and Leder, P., 1981, Human immunoglobulin D segments encoded in tandem multigenic families,Nature 294:631–635.PubMedCrossRefGoogle Scholar
  32. 32.
    Stevens, F. J., Westholm, F. A., Solomon, A., and Schiffer, M., 1980, Self-association of human immunoglobulin kappa I light chains: Role of the third hypervariable region, Proc. Natl. Acad. Sci. USA 77:1144–1148.PubMedCrossRefGoogle Scholar
  33. 33.
    Home, C., Klein, M., Polidoulis, I., and Dorrington, K. J., 1982, Noncovalent association of heavy and light chains of human immunoglobulins. III. Specific interactions between VH and VL, J. Immunol. 129:660–664.Google Scholar
  34. 34.
    Rudikoff, S., Satow, Y., Padlan, E., Davies, D., and Potter, M., 1981, Kappa chain structure from a crystallized murine Fab’: Role of joining segment in hapten binding, J. Mol. Immunol. 18:705–711.CrossRefGoogle Scholar
  35. 35.
    Cook, W. D., Rudikoff, S., Giusti, A., and Scharff, M. D., 1982, Somatic mutation in a cultured mouse myeloma cell affects antigen binding, Proc. Natl. Acad. Sci. USA 79:1240–1244.PubMedCrossRefGoogle Scholar
  36. 36.
    Rudikoff, S., Giusti, A. M., Cook, W. D., and Scharff, M. D., 1982, Single amino acid substitution altering antigen-binding specificity, Proc. Natl. Acad. Sci. USA 79:1979–1983.PubMedCrossRefGoogle Scholar
  37. 37.
    Edmundson, A. B., Ely, K. R., and Hurron, J. N., 1984, A search for site-filling ligands in the Meg Bence-Jones dimer: Crystal binding studies of fluorescent compounds, Mol. Immunol. 21:561–576.PubMedCrossRefGoogle Scholar
  38. 38.
    Kabat, E. A., 1966, TheNatureof an antigenic determinant, J. Immunol. 97:1–11.PubMedGoogle Scholar
  39. 39.
    Go, K., Kartha, G., and Chen, J. P., 1980, Structure of digoxin, Acta Cryst. B 36:1811–1819.CrossRefGoogle Scholar
  40. 40.
    Fieser, L. F., and Fieser, M., 1959, Cardiac-active principles, in: Steroids, Reinhold, New York, pp. 727–809.Google Scholar
  41. 41.
    Smith, T. W., Butler, V. P., and Haber, E., 1970, Characterization of antibodies of high affinity and specificity to the digitalis glycoside digoxin, Biochemistry 9:331–337.PubMedCrossRefGoogle Scholar
  42. 42.
    Mudgett-Hunter, M., Margolies, M. N, Ju, A., Haber, E., 1982, High-affinity monoclonal antibodies to the cardiac glycoside digoxin, J. Immunol. 129:1165–1172.Google Scholar
  43. 43.
    Köhler, G., and Milstein, C., 1975, Continuous cultures of fused cells secreting antibody of predefined specificity,Nature 256:495–497.PubMedCrossRefGoogle Scholar
  44. 44.
    Klinman, N. R., Pickard, A. R., Sigal, N. H., Gearhart, P. J., Metcalf, E. S., and Pierce, S. K., 1976, Assessing B cell diversification by antigen receptor and precursor cell analysis, Ann. Immunol. (Paris) 127C:489–502.Google Scholar
  45. 45.
    Smith, T. W., 1972, Ouabain specific antibodies and immunochemical properties and reversal of Na-K-ATPase inhibition, J. Clin. Invest. 51:1583–1593.PubMedCrossRefGoogle Scholar
  46. 46.
    Brauer, A. W., Margolies, M. N, and Haber, E., 1975, The application of 0.1 M Quadrol to the microsequence of proteins and the sequence of tryptic peptides, Biochemistry 14:3029–3035.PubMedCrossRefGoogle Scholar
  47. 47.
    Novotný, J., and Margolies, M. N, 1983, Amino acid sequence of light chain variable region from a mouse anti-digoxin hybridoma antibody, Biochemistry 22:1153–1158.PubMedCrossRefGoogle Scholar
  48. 48.
    Margolies, M. N., and Brauer, A. W., 1978, Protein microsequencing using high pressure liquid chromatography of phenylthiohydantoin amino acids, J. Chromatogr. 148:429–439.CrossRefGoogle Scholar
  49. 49.
    Margolies, M. N., Brauer, A. W., Oman, C. L., Klapper, D. G., and Horn, M. J., 1982, Improved automatic conversion for use with a liquid-phase sequencer, in: Proceedings of IVth International Conference on Methods in Protein Sequence Analysis (M. Elzinga, ed.), Humana Press, Clifton, New Jersey, pp. 189–203.CrossRefGoogle Scholar
  50. 50.
    Clarke, S. H., Claflin, J. L., Potter, M., and Rudikoff, S., 1982, Polymorphisms in anti-phosphocholine antibodies reflecting evolution of immunoglobulin gene families, J. Exp. Med. 157:98–113.CrossRefGoogle Scholar
  51. 51.
    Rose, D. R., Seaton, B. A., Petsko, G. A., Novotny, J., Margolies, M. N., Locke, E., and Haber, E., 1983, Crystallization of the Fab fragment of a monoclonal anti-digoxin antibody and its complex with digoxin, J. Mol.Biol. 164:203–206.CrossRefGoogle Scholar
  52. 52.
    Alt, F. W., and Baltimore, D., 1982, Joining of immunoglobulin heavy chain gene segments: Implications from a chromosome with evidence of 3 D-JH fusions, Proc. Natl. Acad. Sci. USA 79:4118–4122.PubMedCrossRefGoogle Scholar
  53. 53.
    Oi, V. T., Morrison, S. L., Herzenberg, L. A., and Berg, P., 1983, Immunoglobulin gene expression in transformed lymphoid cells, Proc. Natl. Acad. Sci. USA 80:825–829.PubMedCrossRefGoogle Scholar
  54. 54.
    Poljak, R. J., Amzel, L. M., Avey, H. P., Becka, L. N., and Nisonoff, A., 1972, Structure of Fab’ NEW at 6 A resolution,Nature New Biol. 235:137–140.PubMedCrossRefGoogle Scholar
  55. 55.
    Dickerson, R. E., 1983, The DNA helix and how it is read, Sci. Am. 246(6):94–111.CrossRefGoogle Scholar
  56. 56.
    Kabat, E. A., Wu, T. T., and Bilofsky, H., 1979, Sequences in immunoglobulin chains: Tabulation and analyses of amino acid sequences of precursors, V-regions, C-regions, J-chains and BP microglobulins, NIH Publication, 80–2008.Google Scholar
  57. 57.
    IUPAC-IUB Commission on Biological Nomenclature, 1968, A one-letter notation for amino acid sequences. Tentative Rules, J. Biol. Chem. 243:3557.Google Scholar
  58. 58.
    Haber, E., and Margolies, M. N., Combining site specificity and idiotypy: A study of antidigoxin and antiarsonate antibodies, in: The Biology of Idiotypes (M. I. Greene and A. Nisonoff, eds.), Plenum Press, New York, pp. 141–170.Google Scholar

Copyright information

© Plenum Press, New York 1985

Authors and Affiliations

  • Edgar Haber
    • 1
    • 2
  • Jiří Novotný
    • 3
    • 4
  1. 1.Cardiac Unit and Cellular and Molecular Research LaboratoryMassachusetts General HospitalBostonUSA
  2. 2.Department of MedicineHarvard Medical SchoolBostonUSA
  3. 3.Cellular and Molecular Research LaboratoryMassachusetts General HospitalBostonUSA
  4. 4.Harvard Medical SchoolBostonUSA

Personalised recommendations