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. 1974 Nov;71(11):4298–4302. doi: 10.1073/pnas.71.11.4298

The Three-Dimensional Structure of a Phosphorylcholine-Binding Mouse Immunoglobulin Fab and the Nature of the Antigen Binding Site

David M Segal *,†, Eduardo A Padlan *, Gerson H Cohen *, Stuart Rudikoff ‡, Michael Potter ‡, David R Davies *
PMCID: PMC433869  PMID: 4530984

Abstract

The structure of the Fab of McPC 603, a mouse myeloma protein with phosphorylcholine binding activity, has been determined to 3.1-Å resoltuion. The four domains are found to be structurally similar with a well-defined double-layer structure. A large cavity exists at one end of the fragment, the walls of which are formed exclusively of hypervariable residues. Phosphorylcholine binds in this cavity and forms specific interactions with several well-defined amino-acid side chains of the protein. The hapten is bound asymmetrically and interacts more with the heavy chain than with the light chain.

Keywords: x-ray diffraction, domain structure, hypervariable cavity, hapten binding, antibody diversity

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Amzel L. M., Poljak R. J., Saul F., Varga J. M., Richards F. F. The three dimensional structure of a combining region-ligand complex of immunoglobulin NEW at 3.5-A resolution. Proc Natl Acad Sci U S A. 1974 Apr;71(4):1427–1430. doi: 10.1073/pnas.71.4.1427. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Barstad P., Rudikoff S., Potter M., Cohn M., Konigsberg W., Hood L. Immunoglobulin structure: amino terminal sequences of mouse myeloma proteins that bind phosphorylcholine. Science. 1974 Mar 8;183(4128):962–966. doi: 10.1126/science.183.4128.962. [DOI] [PubMed] [Google Scholar]
  3. Capra J. D., Kehoe J. M. Variable region sequences of five human immunoglobulin heavy chains of the VH3 subgroup: definitive identification of four heavy chain hypervariable regions. Proc Natl Acad Sci U S A. 1974 Mar;71(3):845–848. doi: 10.1073/pnas.71.3.845. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Edelman G. M., Cunningham B. A., Gall W. E., Gottlieb P. D., Rutishauser U., Waxdal M. J. The covalent structure of an entire gammaG immunoglobulin molecule. Proc Natl Acad Sci U S A. 1969 May;63(1):78–85. doi: 10.1073/pnas.63.1.78. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Epp O., Colman P., Fehlhammer H., Bode W., Schiffer M., Huber R., Palm W. Crystal and molecular structure of a dimer composed of the variable portions of the Bence-Jones protein REI. Eur J Biochem. 1974 Jun 15;45(2):513–524. doi: 10.1111/j.1432-1033.1974.tb03576.x. [DOI] [PubMed] [Google Scholar]
  6. Francis S. H., Leslie R. G., Hood L., Eisen H. N. Amino-acid sequence of the variable region of the heavy (alpha) chain of a mouse myeloma protein with anti-hapten activity. Proc Natl Acad Sci U S A. 1974 Apr;71(4):1123–1127. doi: 10.1073/pnas.71.4.1123. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Gray W. R., Dreyer W. J., Hood L. Mechanism of antibody synthesis: size differences between mouse kappa chains. Science. 1967 Jan 27;155(3761):465–467. doi: 10.1126/science.155.3761.465. [DOI] [PubMed] [Google Scholar]
  8. Lieberman R., Potter M., Mushinski E. B., Humphrey W., Jr, Rudikoff S. Genetics of a new IgVH (T15 idiotype) marker in the mouse regulating natural antibody to phosphorylcholine. J Exp Med. 1974 Apr 1;139(4):983–1001. doi: 10.1084/jem.139.4.983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Padlan E. A., Segal D. M., Spande T. F., Davies D. R., Rudikoff S., Potter M. Structure at 4.5 A resolution of a phosphorylcholine-binding fab. Nat New Biol. 1973 Oct 10;245(145):165–167. doi: 10.1038/newbio245165a0. [DOI] [PubMed] [Google Scholar]
  10. Pilz I., Kratky O., Karush F. Changes of the conformation of rabbit IgG antibody caused by the specific binding of a hapten. X-ray small-angle studies. Eur J Biochem. 1974 Jan 3;41(1):91–96. doi: 10.1111/j.1432-1033.1974.tb03247.x. [DOI] [PubMed] [Google Scholar]
  11. Poljak R. J., Amzel L. M., Avey H. P., Chen B. L., Phizackerley R. P., Saul F. Three-dimensional structure of the Fab' fragment of a human immunoglobulin at 2,8-A resolution. Proc Natl Acad Sci U S A. 1973 Dec;70(12):3305–3310. doi: 10.1073/pnas.70.12.3305. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Potter M. Antigen-binding myeloma proteins in mice. Ann N Y Acad Sci. 1971 Dec 31;190:306–321. doi: 10.1111/j.1749-6632.1971.tb13543.x. [DOI] [PubMed] [Google Scholar]
  13. Potter M. Immunoglobulin-producing tumors and myeloma proteins of mice. Physiol Rev. 1972 Jul;52(3):631–719. doi: 10.1152/physrev.1972.52.3.631. [DOI] [PubMed] [Google Scholar]
  14. Richards F. M. The matching of physical models to three-dimensional electron-density maps: a simple optical device. J Mol Biol. 1968 Oct 14;37(1):225–230. doi: 10.1016/0022-2836(68)90085-5. [DOI] [PubMed] [Google Scholar]
  15. Rosenstein R. W., Musson R. A., Armstrong M. K., Konigsberg W. H., Richards F. F. Contact regions for dinitrophenyl and menadione haptens in an immunoglobulin binding more than one antigen. Proc Natl Acad Sci U S A. 1972 Apr;69(4):877–881. doi: 10.1073/pnas.69.4.877. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Rudikoff S., Potter M., Segal D. M., Padlan E. A., Davies D. R. Crystals of phosphorylcholine-binding Fab-fragments from mouse myeloma proteins: preparation and x-ray analysis. Proc Natl Acad Sci U S A. 1972 Dec;69(12):3689–3692. doi: 10.1073/pnas.69.12.3689. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Rudikoff S., Potter M. Variable region sequence of the heavy chain from a phosphorylcholine binding myeloma protein. Biochemistry. 1974 Sep 10;13(19):4033–4038. doi: 10.1021/bi00716a034. [DOI] [PubMed] [Google Scholar]
  18. Schiffer M., Girling R. L., Ely K. R., Edmundson A. B. Structure of a lambda-type Bence-Jones protein at 3.5-A resolution. Biochemistry. 1973 Nov 6;12(23):4620–4631. doi: 10.1021/bi00747a013. [DOI] [PubMed] [Google Scholar]
  19. Svasti J., Milstein C. The complete amino acid sequence of a mouse kappa light chain. Biochem J. 1972 Jun;128(2):427–444. doi: 10.1042/bj1280427. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Venkatachalam C. M. Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers. 1968 Oct;6(10):1425–1436. doi: 10.1002/bip.1968.360061006. [DOI] [PubMed] [Google Scholar]
  21. Wu T. T., Kabat E. A. 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. 1970 Aug 1;132(2):211–250. doi: 10.1084/jem.132.2.211. [DOI] [PMC free article] [PubMed] [Google Scholar]

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