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. 1992 Sep;1(9):1154–1161. doi: 10.1002/pro.5560010909

Three-dimensional structure of the Fab fragment of a neutralizing antibody to human rhinovirus serotype 2.

J Tormo 1, E Stadler 1, T Skern 1, H Auer 1, O Kanzler 1, C Betzel 1, D Blaas 1, I Fita 1
PMCID: PMC2142184  PMID: 1338980

Abstract

The crystal structure of the antigen-binding fragment of a monoclonal antibody (8F5) that neutralizes human rhinovirus serotype 2 has been determined by X-ray diffraction studies. Antibody 8F5, obtained by immunization with native HRV2 virions, cross-reacts with peptides of the viral capsid protein VP2, which contribute to the neutralizing immunogenic site B in this serotype. The structure was solved by the molecular replacement method and has been refined to an R-factor of 18.9% at 2.8 A resolution. The elbow angle, relating the variable and constant modules of the molecule is 127 degrees, representing the smallest elbow angle observed so far in an Fab fragment. Furthermore, the charged residues of the epitope can be well accommodated in the antigen-binding site. This is the first crystal structure reported for an antibody directed against an icosahedral virus.

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Selected References

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  1. Altenburger W., Neumaier P. S., Steinmetz M., Zachau H. G. DNA sequence of the constant gene region of the mouse immunoglobulin kappa chain. Nucleic Acids Res. 1981 Feb 25;9(4):971–981. doi: 10.1093/nar/9.4.971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Alzari P. M., Lascombe M. B., Poljak R. J. Three-dimensional structure of antibodies. Annu Rev Immunol. 1988;6:555–580. doi: 10.1146/annurev.iy.06.040188.003011. [DOI] [PubMed] [Google Scholar]
  3. Alzari P. M., Spinelli S., Mariuzza R. A., Boulot G., Poljak R. J., Jarvis J. M., Milstein C. Three-dimensional structure determination of an anti-2-phenyloxazolone antibody: the role of somatic mutation and heavy/light chain pairing in the maturation of an immune response. EMBO J. 1990 Dec;9(12):3807–3814. doi: 10.1002/j.1460-2075.1990.tb07598.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Amzel L. M., Poljak R. J. Three-dimensional structure of immunoglobulins. Annu Rev Biochem. 1979;48:961–997. doi: 10.1146/annurev.bi.48.070179.004525. [DOI] [PubMed] [Google Scholar]
  5. Appleyard G., Russell S. M., Clarke B. E., Speller S. A., Trowbridge M., Vadolas J. Neutralization epitopes of human rhinovirus type 2. J Gen Virol. 1990 Jun;71(Pt 6):1275–1282. doi: 10.1099/0022-1317-71-6-1275. [DOI] [PubMed] [Google Scholar]
  6. Bjorkman P. J., Saper M. A., Samraoui B., Bennett W. S., Strominger J. L., Wiley D. C. Structure of the human class I histocompatibility antigen, HLA-A2. Nature. 1987 Oct 8;329(6139):506–512. doi: 10.1038/329506a0. [DOI] [PubMed] [Google Scholar]
  7. Chang C. H., Short M. T., Westholm F. A., Stevens F. J., Wang B. C., Furey W., Jr, Solomon A., Schiffer M. Novel arrangement of immunoglobulin variable domains: X-ray crystallographic analysis of the lambda-chain dimer Bence-Jones protein Loc. Biochemistry. 1985 Aug 27;24(18):4890–4897. doi: 10.1021/bi00339a025. [DOI] [PubMed] [Google Scholar]
  8. Cygler M., Anderson W. F. Application of the molecular replacement method to multidomain proteins. 2. Comparison of various methods for positioning an oriented fragment in the unit cell. Acta Crystallogr A. 1988 May 1;44(Pt 3):300–308. doi: 10.1107/s0108767387012236. [DOI] [PubMed] [Google Scholar]
  9. Cygler M., Boodhoo A., Lee J. S., Anderson W. F. Crystallization and structure determination of an autoimmune anti-poly(dT) immunoglobulin Fab fragment at 3.0 A resolution. J Biol Chem. 1987 Jan 15;262(2):643–648. [PubMed] [Google Scholar]
  10. Ely K. R., Firca J. R., Williams K. J., Abola E. E., Fenton J. M., Schiffer M., Panagiotopoulos N. C., Edmundson A. B. Crystal properties as indicators of conformational changes during ligand binding or interconversion of Mcg light chain isomers. Biochemistry. 1978 Jan 10;17(1):158–167. doi: 10.1021/bi00594a023. [DOI] [PubMed] [Google Scholar]
  11. Francis M. J., Hastings G. Z., Sangar D. V., Clark R. P., Syred A., Clarke B. E., Rowlands D. J., Brown F. A synthetic peptide which elicits neutralizing antibody against human rhinovirus type 2. J Gen Virol. 1987 Oct;68(Pt 10):2687–2691. doi: 10.1099/0022-1317-68-10-2687. [DOI] [PubMed] [Google Scholar]
  12. Hendrickson W. A. Stereochemically restrained refinement of macromolecular structures. Methods Enzymol. 1985;115:252–270. doi: 10.1016/0076-6879(85)15021-4. [DOI] [PubMed] [Google Scholar]
  13. Jones T. A. Diffraction methods for biological macromolecules. Interactive computer graphics: FRODO. Methods Enzymol. 1985;115:157–171. doi: 10.1016/0076-6879(85)15014-7. [DOI] [PubMed] [Google Scholar]
  14. Lascombe M. B., Alzari P. M., Boulot G., Saludjian P., Tougard P., Berek C., Haba S., Rosen E. M., Nisonoff A., Poljak R. J. Three-dimensional structure of Fab R19.9, a monoclonal murine antibody specific for the p-azobenzenearsonate group. Proc Natl Acad Sci U S A. 1989 Jan;86(2):607–611. doi: 10.1073/pnas.86.2.607. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. LeBoeuf R. D., Galin F. S., Hollinger S. K., Peiper S. C., Blalock J. E. Cloning and sequencing of immunoglobulin variable-region genes using degenerate oligodeoxyribonucleotides and polymerase chain reaction. Gene. 1989 Oct 30;82(2):371–377. doi: 10.1016/0378-1119(89)90065-6. [DOI] [PubMed] [Google Scholar]
  16. Mian I. S., Bradwell A. R., Olson A. J. Structure, function and properties of antibody binding sites. J Mol Biol. 1991 Jan 5;217(1):133–151. doi: 10.1016/0022-2836(91)90617-f. [DOI] [PubMed] [Google Scholar]
  17. Padlan E. A. On the nature of antibody combining sites: unusual structural features that may confer on these sites an enhanced capacity for binding ligands. Proteins. 1990;7(2):112–124. doi: 10.1002/prot.340070203. [DOI] [PubMed] [Google Scholar]
  18. Rini J. M., Schulze-Gahmen U., Wilson I. A. Structural evidence for induced fit as a mechanism for antibody-antigen recognition. Science. 1992 Feb 21;255(5047):959–965. doi: 10.1126/science.1546293. [DOI] [PubMed] [Google Scholar]
  19. Rossmann M. G., Arnold E., Erickson J. W., Frankenberger E. A., Griffith J. P., Hecht H. J., Johnson J. E., Kamer G., Luo M., Mosser A. G. Structure of a human common cold virus and functional relationship to other picornaviruses. Nature. 1985 Sep 12;317(6033):145–153. doi: 10.1038/317145a0. [DOI] [PubMed] [Google Scholar]
  20. Sibanda B. L., Blundell T. L., Thornton J. M. Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering. J Mol Biol. 1989 Apr 20;206(4):759–777. doi: 10.1016/0022-2836(89)90583-4. [DOI] [PubMed] [Google Scholar]
  21. Skern T., Neubauer C., Frasel L., Gründler P., Sommergruber W., Zorn M., Kuechler E., Blaas D. A neutralizing epitope on human rhinovirus type 2 includes amino acid residues between 153 and 164 of virus capsid protein VP2. J Gen Virol. 1987 Feb;68(Pt 2):315–323. doi: 10.1099/0022-1317-68-2-315. [DOI] [PubMed] [Google Scholar]
  22. Stanway G. Structure, function and evolution of picornaviruses. J Gen Virol. 1990 Nov;71(Pt 11):2483–2501. doi: 10.1099/0022-1317-71-11-2483. [DOI] [PubMed] [Google Scholar]
  23. Strong R. K., Campbell R., Rose D. R., Petsko G. A., Sharon J., Margolies M. N. Three-dimensional structure of murine anti-p-azophenylarsonate Fab 36-71. 1. X-ray crystallography, site-directed mutagenesis, and modeling of the complex with hapten. Biochemistry. 1991 Apr 16;30(15):3739–3748. doi: 10.1021/bi00229a022. [DOI] [PubMed] [Google Scholar]
  24. Tormo J., Fita I., Kanzler O., Blaas D. Crystallization and preliminary x-ray diffraction studies of the Fab fragment of a neutralizing monoclonal antibody directed against human rhinovirus serotype 2. J Biol Chem. 1990 Oct 5;265(28):16799–16800. [PubMed] [Google Scholar]
  25. Yamawaki-Kataoka Y., Miyata T., Honjo T. The complete nucleotide sequence of mouse immunoglobin gamma 2a gene and evolution of heavy chain genes: further evidence for intervening sequence-mediated domain transfer. Nucleic Acids Res. 1981 Mar 25;9(6):1365–1381. doi: 10.1093/nar/9.6.1365. [DOI] [PMC free article] [PubMed] [Google Scholar]

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