Skip to main content
The EMBO Journal logoLink to The EMBO Journal
. 1992 Sep;11(9):3193–3201. doi: 10.1002/j.1460-2075.1992.tb05396.x

Three-dimensional crystal structure of recombinant murine interferon-beta.

T Senda 1, T Shimazu 1, S Matsuda 1, G Kawano 1, H Shimizu 1, K T Nakamura 1, Y Mitsui 1
PMCID: PMC556852  PMID: 1505514

Abstract

The crystal structure of recombinant murine interferon-beta (IFN-beta) has been solved by the multiple isomorphous replacement method and refined to an R-factor of 20.5% against 2.6 A X-ray diffraction data. The structure shows a variant of the alpha-helix bundle with a new chain-folding topology, which seems to represent a basic structural framework of all the IFN-alpha and IFN-beta molecules belonging to the type I family. Functionally important segments of the polypeptide chain, as implied through numerous gene manipulation studies carried out so far, are spatially clustered indicating the binding site(s) to the receptor(s). Comparison of the present structure with those of other alpha-helical cytokine proteins, including porcine growth hormone, interleukin 2 and interferon gamma, indicated either a topological similarity in chain folding or a similar spatial arrangement of the alpha-helices.

Full text

PDF
3193

Images in this article

Selected References

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

  1. Abdel-Meguid S. S., Shieh H. S., Smith W. W., Dayringer H. E., Violand B. N., Bentle L. A. Three-dimensional structure of a genetically engineered variant of porcine growth hormone. Proc Natl Acad Sci U S A. 1987 Sep;84(18):6434–6437. doi: 10.1073/pnas.84.18.6434. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Arnheiter H., Ohno M., Smith M., Gutte B., Zoon K. C. Orientation of a human leukocyte interferon molecule on its cell surface receptor: carboxyl terminus remains accessible to a monoclonal antibody made against a synthetic interferon fragment. Proc Natl Acad Sci U S A. 1983 May;80(9):2539–2543. doi: 10.1073/pnas.80.9.2539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Baldwin E. T., Weber I. T., St Charles R., Xuan J. C., Appella E., Yamada M., Matsushima K., Edwards B. F., Clore G. M., Gronenborn A. M. Crystal structure of interleukin 8: symbiosis of NMR and crystallography. Proc Natl Acad Sci U S A. 1991 Jan 15;88(2):502–506. doi: 10.1073/pnas.88.2.502. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bazan J. F. Haemopoietic receptors and helical cytokines. Immunol Today. 1990 Oct;11(10):350–354. doi: 10.1016/0167-5699(90)90139-z. [DOI] [PubMed] [Google Scholar]
  5. Bazan J. F. Neuropoietic cytokines in the hematopoietic fold. Neuron. 1991 Aug;7(2):197–208. doi: 10.1016/0896-6273(91)90258-2. [DOI] [PubMed] [Google Scholar]
  6. Bazan J. F. Structural design and molecular evolution of a cytokine receptor superfamily. Proc Natl Acad Sci U S A. 1990 Sep;87(18):6934–6938. doi: 10.1073/pnas.87.18.6934. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Beilharz M. W., Tymms M. J., Chambers P. J., McInnes B., Pitha-Rowe P. M., Linnane A. W. Amino acid substitutions which alter the antiviral activity of human interferon-alpha 1 on mouse cells. J Interferon Res. 1988 Dec;8(6):779–782. doi: 10.1089/jir.1988.8.779. [DOI] [PubMed] [Google Scholar]
  8. Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  9. Brandhuber B. J., Boone T., Kenney W. C., McKay D. B. Three-dimensional structure of interleukin-2. Science. 1987 Dec 18;238(4834):1707–1709. doi: 10.1126/science.3500515. [DOI] [PubMed] [Google Scholar]
  10. Breiter D. R., Kanost M. R., Benning M. M., Wesenberg G., Law J. H., Wells M. A., Rayment I., Holden H. M. Molecular structure of an apolipoprotein determined at 2.5-A resolution. Biochemistry. 1991 Jan 22;30(3):603–608. doi: 10.1021/bi00217a002. [DOI] [PubMed] [Google Scholar]
  11. Brünger A. T., Kuriyan J., Karplus M. Crystallographic R factor refinement by molecular dynamics. Science. 1987 Jan 23;235(4787):458–460. doi: 10.1126/science.235.4787.458. [DOI] [PubMed] [Google Scholar]
  12. Camble R., Petter N. N., Trueman P., Newton C. R., Carr F. J., Hockney R. C., Moore V. E., Greene A. R., Holland D., Edge M. D. Functionally important conserved amino-acids in interferon-alpha 2 identified with analogues produced from synthetic genes. Biochem Biophys Res Commun. 1986 Feb 13;134(3):1404–1411. doi: 10.1016/0006-291x(86)90405-5. [DOI] [PubMed] [Google Scholar]
  13. Cheetham B. F., McInnes B., Mantamadiotis T., Murray P. J., Alin P., Bourke P., Linnane A. W., Tymms M. J. Structure-function studies of human interferons-alpha: enhanced activity on human and murine cells. Antiviral Res. 1991 Jan;15(1):27–39. doi: 10.1016/0166-3542(91)90038-s. [DOI] [PubMed] [Google Scholar]
  14. Colamonici O. R., Pfeffer L. M., D'Alessandro F., Platanias L. C., Gregory S. A., Rosolen A., Nordan R., Cruciani R. A., Diaz M. O. Multichain structure of the IFN-alpha receptor on hematopoietic cells. J Immunol. 1992 Apr 1;148(7):2126–2132. [PubMed] [Google Scholar]
  15. Cunningham B. C., Ultsch M., De Vos A. M., Mulkerrin M. G., Clauser K. R., Wells J. A. Dimerization of the extracellular domain of the human growth hormone receptor by a single hormone molecule. Science. 1991 Nov 8;254(5033):821–825. doi: 10.1126/science.1948064. [DOI] [PubMed] [Google Scholar]
  16. Cunningham B. C., Wells J. A. High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis. Science. 1989 Jun 2;244(4908):1081–1085. doi: 10.1126/science.2471267. [DOI] [PubMed] [Google Scholar]
  17. Cunningham B. C., Wells J. A. Rational design of receptor-specific variants of human growth hormone. Proc Natl Acad Sci U S A. 1991 Apr 15;88(8):3407–3411. doi: 10.1073/pnas.88.8.3407. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Day C., Schwartz B., Li B. L., Pestka S. Engineered disulfide bond greatly increases specific activity of recombinant murine interferon-beta. J Interferon Res. 1992 Apr;12(2):139–143. doi: 10.1089/jir.1992.12.139. [DOI] [PubMed] [Google Scholar]
  19. DeGrado W. F., Wasserman Z. R., Chowdhry V. Sequence and structural homologies among type I and type II interferons. Nature. 1982 Nov 25;300(5890):379–381. doi: 10.1038/300379a0. [DOI] [PubMed] [Google Scholar]
  20. Diederichs K., Boone T., Karplus P. A. Novel fold and putative receptor binding site of granulocyte-macrophage colony-stimulating factor. Science. 1991 Dec 20;254(5039):1779–1782. doi: 10.1126/science.1837174. [DOI] [PubMed] [Google Scholar]
  21. Ealick S. E., Cook W. J., Vijay-Kumar S., Carson M., Nagabhushan T. L., Trotta P. P., Bugg C. E. Three-dimensional structure of recombinant human interferon-gamma. Science. 1991 May 3;252(5006):698–702. doi: 10.1126/science.1902591. [DOI] [PubMed] [Google Scholar]
  22. Eck M. J., Sprang S. R. The structure of tumor necrosis factor-alpha at 2.6 A resolution. Implications for receptor binding. J Biol Chem. 1989 Oct 15;264(29):17595–17605. doi: 10.2210/pdb1tnf/pdb. [DOI] [PubMed] [Google Scholar]
  23. Eriksson A. E., Cousens L. S., Weaver L. H., Matthews B. W. Three-dimensional structure of human basic fibroblast growth factor. Proc Natl Acad Sci U S A. 1991 Apr 15;88(8):3441–3445. doi: 10.1073/pnas.88.8.3441. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Finzel B. C., Clancy L. L., Holland D. R., Muchmore S. W., Watenpaugh K. D., Einspahr H. M. Crystal structure of recombinant human interleukin-1 beta at 2.0 A resolution. J Mol Biol. 1989 Oct 20;209(4):779–791. doi: 10.1016/0022-2836(89)90606-2. [DOI] [PubMed] [Google Scholar]
  25. Fish E. N., Banerjee K., Stebbing N. The role of three domains in the biological activity of human interferon-alpha. J Interferon Res. 1989 Feb;9(1):97–114. doi: 10.1089/jir.1989.9.97. [DOI] [PubMed] [Google Scholar]
  26. Hibino Y., Kumar C. S., Mariano T. M., Lai D. H., Pestka S. Chimeric interferon-gamma receptors demonstrate that an accessory factor required for activity interacts with the extracellular domain. J Biol Chem. 1992 Feb 25;267(6):3741–3749. [PubMed] [Google Scholar]
  27. Higashi Y., Sokawa Y., Watanabe Y., Kawade Y., Ohno S., Takaoka C., Taniguchi T. Structure and expression of a cloned cDNA for mouse interferon-beta. J Biol Chem. 1983 Aug 10;258(15):9522–9529. [PubMed] [Google Scholar]
  28. Hirono S., Nakamura K. T., Iitaka Y., Mitsui Y. Crystal structure of the complex of subtilisin BPN' with its protein inhibitor Streptomyces subtilisin inhibitor. The structure at 4.3 Angstroms resolution. J Mol Biol. 1979 Jul 15;131(4):855–869. doi: 10.1016/0022-2836(79)90205-5. [DOI] [PubMed] [Google Scholar]
  29. ISAACS A., LINDENMANN J. Virus interference. I. The interferon. Proc R Soc Lond B Biol Sci. 1957 Sep 12;147(927):258–267. doi: 10.1098/rspb.1957.0048. [DOI] [PubMed] [Google Scholar]
  30. Jones E. Y., Stuart D. I., Walker N. P. Structure of tumour necrosis factor. Nature. 1989 Mar 16;338(6212):225–228. doi: 10.1038/338225a0. [DOI] [PubMed] [Google Scholar]
  31. Kerry J. A., Tymms M. J., Linnane A. W. Conserved amino acid residues arginine 33 and tyrosine 123 are critical for the antiviral activity of murine interferon-alpha 1. Biochem Biophys Res Commun. 1988 Sep 15;155(2):714–719. doi: 10.1016/s0006-291x(88)80553-9. [DOI] [PubMed] [Google Scholar]
  32. Kontsek P., Borecky L., Kontsekova E., Macikova I., Kolcunova A., Novak M., Krchnak V. Mapping of two immunodominant structures on human interferon alpha 2c and their role in binding to cells. Mol Immunol. 1991 Nov;28(11):1289–1297. doi: 10.1016/0161-5890(91)90016-d. [DOI] [PubMed] [Google Scholar]
  33. Langer J. A., Pestka S. Structure of interferons. Pharmacol Ther. 1985;27(3):371–401. doi: 10.1016/0163-7258(85)90076-2. [DOI] [PubMed] [Google Scholar]
  34. Levy W. P., Rubinstein M., Shively J., Del Valle U., Lai C. Y., Moschera J., Brink L., Gerber L., Stein S., Pestka S. Amino acid sequence of a human leukocyte interferon. Proc Natl Acad Sci U S A. 1981 Oct;78(10):6186–6190. doi: 10.1073/pnas.78.10.6186. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Lydon N. B., Favre C., Bove S., Neyret O., Benureau S., Levine A. M., Seelig G. F., Nagabhushan T. L., Trotta P. P. Immunochemical mapping of alpha-2 interferon. Biochemistry. 1985 Jul 16;24(15):4131–4141. doi: 10.1021/bi00336a048. [DOI] [PubMed] [Google Scholar]
  36. Matsuda S., Kawano G., Itoh S., Mitsui Y., Iitaka Y. Crystallization and preliminary X-ray studies of recombinant murine interferon-beta. J Biol Chem. 1986 Dec 5;261(34):16207–16209. [PubMed] [Google Scholar]
  37. Matsuda S., Senda T., Itoh S., Kawano G., Mizuno H., Mitsui Y. New crystal form of recombinant murine interferon-beta. J Biol Chem. 1989 Aug 15;264(23):13381–13382. [PubMed] [Google Scholar]
  38. Matsuda S., Utsumi J., Kawano G. Purification and characterization of recombinant mouse interferon-beta. J Interferon Res. 1986 Oct;6(5):519–526. doi: 10.1089/jir.1986.6.519. [DOI] [PubMed] [Google Scholar]
  39. McInnes B., Chambers P. J., Cheetham B. F., Beilharz M. W., Tymms M. J. Structure-function studies of interferons-alpha: amino acid substitutions at the conserved residue tyrosine 123 in human interferon-alpha 1. J Interferon Res. 1989 Jun;9(3):305–314. doi: 10.1089/jir.1989.9.305. [DOI] [PubMed] [Google Scholar]
  40. Miller D. L., Kung H. F., Pestka S. Crystallization of recombinant human leukocyte interferon A. Science. 1982 Feb 5;215(4533):689–690. doi: 10.1126/science.6173922. [DOI] [PubMed] [Google Scholar]
  41. Morehead H., Johnston P. D., Wetzel R. Roles of the 29-138 disulfide bond of subtype A of human alpha interferon in its antiviral activity and conformational stability. Biochemistry. 1984 May 22;23(11):2500–2507. doi: 10.1021/bi00306a028. [DOI] [PubMed] [Google Scholar]
  42. NAGANO Y., KOJIMA Y. Inhibition de l'infection vaccinale par un facteur liquide dans le tissu infecté par le virus homologue. C R Seances Soc Biol Fil. 1958;152(11):1627–1629. [PubMed] [Google Scholar]
  43. NAGANO Y., KOJIMA Y. Pouvoir immunisant du virus vaccinal inactivé par des rayons ultraviolets. C R Seances Soc Biol Fil. 1954 Oct;148(19-20):1700–1702. [PubMed] [Google Scholar]
  44. Nicola N. A. Hemopoietic cell growth factors and their receptors. Annu Rev Biochem. 1989;58:45–77. doi: 10.1146/annurev.bi.58.070189.000401. [DOI] [PubMed] [Google Scholar]
  45. Pestka S., Langer J. A., Zoon K. C., Samuel C. E. Interferons and their actions. Annu Rev Biochem. 1987;56:727–777. doi: 10.1146/annurev.bi.56.070187.003455. [DOI] [PubMed] [Google Scholar]
  46. Presnell S. R., Cohen F. E. Topological distribution of four-alpha-helix bundles. Proc Natl Acad Sci U S A. 1989 Sep;86(17):6592–6596. doi: 10.1073/pnas.86.17.6592. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Priestle J. P., Schär H. P., Grütter M. G. Crystallographic refinement of interleukin 1 beta at 2.0 A resolution. Proc Natl Acad Sci U S A. 1989 Dec;86(24):9667–9671. doi: 10.1073/pnas.86.24.9667. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Raj N. B., Israeli R., Kelley K. A., Leach S. J., Minasian E., Sikaris K., Parry D. A., Pitha P. M. Synthesis, antiviral activity, and conformational characterization of mouse-human alpha-interferon hybrids. J Biol Chem. 1988 Jun 25;263(18):8943–8952. [PubMed] [Google Scholar]
  49. Redfield C., Smith L. J., Boyd J., Lawrence G. M., Edwards R. G., Smith R. A., Dobson C. M. Secondary structure and topology of human interleukin 4 in solution. Biochemistry. 1991 Nov 19;30(46):11029–11035. doi: 10.1021/bi00110a004. [DOI] [PubMed] [Google Scholar]
  50. Redlich P. N., Hoeprich P. D., Jr, Colby C. B., Grossberg S. E. Antibodies that neutralize human beta interferon biologic activity recognize a linear epitope: analysis by synthetic peptide mapping. Proc Natl Acad Sci U S A. 1991 May 1;88(9):4040–4044. doi: 10.1073/pnas.88.9.4040. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Samudzi C. T., Burton L. E., Rubin J. R. Crystal structure of recombinant rabbit interferon-gamma at 2.7-A resolution. J Biol Chem. 1991 Nov 15;266(32):21791–21797. [PubMed] [Google Scholar]
  52. Streuli M., Hall A., Boll W., Stewart W. E., 2nd, Nagata S., Weissmann C. Target cell specificity of two species of human interferon-alpha produced in Escherichia coli and of hybrid molecules derived from them. Proc Natl Acad Sci U S A. 1981 May;78(5):2848–2852. doi: 10.1073/pnas.78.5.2848. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Takeuchi Y., Satow Y., Nakamura K. T., Mitsui Y. Refined crystal structure of the complex of subtilisin BPN' and Streptomyces subtilisin inhibitor at 1.8 A resolution. J Mol Biol. 1991 Sep 5;221(1):309–325. [PubMed] [Google Scholar]
  54. Tanaka T., Naruto M., Kawano G. Production of recombinant mouse beta-interferon. J Interferon Res. 1986 Aug;6(4):429–435. doi: 10.1089/jir.1986.6.429. [DOI] [PubMed] [Google Scholar]
  55. Tymms M. J., McInnes B., Waine G. J., Cheetham B. F., Linnane A. W. Functional significance of amino acid residues within conserved hydrophilic regions in human interferons-alpha. Antiviral Res. 1989 Aug;12(1):37–47. doi: 10.1016/0166-3542(89)90066-1. [DOI] [PubMed] [Google Scholar]
  56. Utsumi J., Yamazaki S., Hosoi K., Kimura S., Hanada K., Shimazu T., Shimizu H. Characterization of E. coli-derived recombinant human interferon-beta as compared with fibroblast human interferon-beta. J Biochem. 1987 May;101(5):1199–1208. doi: 10.1093/oxfordjournals.jbchem.a121984. [DOI] [PubMed] [Google Scholar]
  57. Uzé G., Lutfalla G., Gresser I. Genetic transfer of a functional human interferon alpha receptor into mouse cells: cloning and expression of its cDNA. Cell. 1990 Jan 26;60(2):225–234. doi: 10.1016/0092-8674(90)90738-z. [DOI] [PubMed] [Google Scholar]
  58. Valenzuela D., Weber H., Weissmann C. Is sequence conservation in interferons due to selection for functional proteins? Nature. 1985 Feb 21;313(6004):698–700. doi: 10.1038/313698a0. [DOI] [PubMed] [Google Scholar]
  59. Van Heuvel M., Bosveld I. J., Klaassen P., Zwarthoff E. C., Trapman J. Structure-function analysis of murine interferon-alpha: antiviral properties of novel hybrid interferons. J Interferon Res. 1988 Feb;8(1):5–14. doi: 10.1089/jir.1988.8.5. [DOI] [PubMed] [Google Scholar]
  60. Vijay-Kumar S., Senadhi S. E., Ealick S. E., Nagabhushan T. L., Trotta P. P., Kosecki R., Reichert P., Bugg C. E. Crystallization and preliminary X-ray investigation of a recombinant form of human gamma-interferon. J Biol Chem. 1987 Apr 5;262(10):4804–4805. [PubMed] [Google Scholar]
  61. Weber H., Valenzuela D., Lujber G., Gubler M., Weissmann C. Single amino acid changes that render human IFN-alpha 2 biologically active on mouse cells. EMBO J. 1987 Mar;6(3):591–598. doi: 10.1002/j.1460-2075.1987.tb04795.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Weber P. C., Salemme F. R. Structural and functional diversity in 4-alpha-helical proteins. Nature. 1980 Sep 4;287(5777):82–84. doi: 10.1038/287082a0. [DOI] [PubMed] [Google Scholar]
  63. Weissmann C., Weber H. The interferon genes. Prog Nucleic Acid Res Mol Biol. 1986;33:251–300. doi: 10.1016/s0079-6603(08)60026-4. [DOI] [PubMed] [Google Scholar]
  64. Zhang J. D., Cousens L. S., Barr P. J., Sprang S. R. Three-dimensional structure of human basic fibroblast growth factor, a structural homolog of interleukin 1 beta. Proc Natl Acad Sci U S A. 1991 Apr 15;88(8):3446–3450. doi: 10.1073/pnas.88.8.3446. [DOI] [PMC free article] [PubMed] [Google Scholar]
  65. Zhang Z. Q., Fournier A., Tan Y. H. The isolation of human beta-interferon receptor by wheat germ lectin affinity and immunosorbent column chromatographies. J Biol Chem. 1986 Jun 15;261(17):8017–8021. [PubMed] [Google Scholar]
  66. de Vos A. M., Ultsch M., Kossiakoff A. A. Human growth hormone and extracellular domain of its receptor: crystal structure of the complex. Science. 1992 Jan 17;255(5042):306–312. doi: 10.1126/science.1549776. [DOI] [PubMed] [Google Scholar]

Articles from The EMBO Journal are provided here courtesy of Nature Publishing Group

RESOURCES