An αβ T cell receptor structure at 2.5 Å and its orientation in the TCR-MHC complex

Science

Volumn 274, Issue 5285, 1996, Pages 209-219

  Garcia, K Christopher ^a   Degano, Massimo ^a   Stanfield, Robyn L ^a   Brunmark, Anders ^b   Jackson, Michael R ^b   Peterson, Per A ^b   Teyton, Luc ^b   Wilson, Ian A ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b JOHNSON AND JOHNSON PHARMACEUTICAL RESEARCH AND DEVELOPMENT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; T LYMPHOCYTE RECEPTOR ALPHA CHAIN; T LYMPHOCYTE RECEPTOR BETA CHAIN; H 2KB PROTEIN, MOUSE; H-2KB PROTEIN, MOUSE; H2 ANTIGEN; LYMPHOCYTE ANTIGEN RECEPTOR; PEPTIDE; RECOMBINANT PROTEIN;

ANTIBODY COMBINING SITE; ANTIGEN RECOGNITION; ARTICLE; CRYSTAL STRUCTURE; GLYCOSYLATION; IMMUNOGLOBULIN GENE; IMMUNOGLOBULIN VARIABLE REGION; MAJOR HISTOCOMPATIBILITY COMPLEX; PRIORITY JOURNAL; PROTEIN DOMAIN; STEREOCHEMISTRY; T LYMPHOCYTE RECEPTOR GENE; X RAY CRYSTALLOGRAPHY; ANIMAL; CARBOHYDRATE ANALYSIS; CELL CULTURE; CHEMICAL STRUCTURE; CHEMISTRY; CRYSTALLIZATION; CYTOTOXIC T LYMPHOCYTE; DROSOPHILA MELANOGASTER; HYDROGEN BOND; IMMUNOLOGY; METABOLISM; MOLECULAR GENETICS; MOUSE; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE;

ANIMALS; CARBOHYDRATE SEQUENCE; CELLS, CULTURED; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; DROSOPHILA MELANOGASTER; GLYCOSYLATION; H-2 ANTIGENS; HYDROGEN BONDING; MAJOR HISTOCOMPATIBILITY COMPLEX; MICE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; RECEPTORS, ANTIGEN, T-CELL, ALPHA-BETA; RECOMBINANT PROTEINS; T-LYMPHOCYTES, CYTOTOXIC;

EID: 0029662223     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.274.5285.209     Document Type: Article

References (122)

1. D.H. Katz, T. Hamaoka, B. Benacerraf, J. Exp. Med. 137, 1405 (1973); E. M. Shevach and A. S. Rosenthal, ibid. 138, 1213 (1973); P. C. Doherty, R. V. Blanden, R. M. Zinkernagel, Transplant. Rev. 29, 89 (1976).
2. D.H. Katz, T. Hamaoka, B. Benacerraf, J. Exp. Med. 137, 1405 (1973); E. M. Shevach and A. S. Rosenthal, ibid. 138, 1213 (1973); P. C. Doherty, R. V. Blanden, R. M. Zinkernagel, Transplant. Rev. 29, 89 (1976).
3. D.H. Katz, T. Hamaoka, B. Benacerraf, J. Exp. Med. 137, 1405 (1973); E. M. Shevach and A. S. Rosenthal, ibid. 138, 1213 (1973); P. C. Doherty, R. V. Blanden, R. M. Zinkernagel, Transplant. Rev. 29, 89 (1976).
4. H. Clevers, B, Alarcon, T. Wileman, C. A. Terhorst, Annu. Rev. Immunol. 6, 629 (1988).
5. H. Saito et al., Nature 312, 36 (1984) [cloning of 2C α chain]; S. M. Hedrick, D. I. Cohen, E. A. Nielsen, M. M. Davis, ibid. 308, 149 (1984); S. M. Hedrick, E. A. Nielsen, J. Kavaler, D. I. Cohen, M. M. Davis, ibid., p. 153; Y. Yangi et al., ibid., p. 145; Y. Chien et al., ibid. 312, 31 (1984).
6. H. Saito et al., Nature 312, 36 (1984) [cloning of 2C α chain]; S. M. Hedrick, D. I. Cohen, E. A. Nielsen, M. M. Davis, ibid. 308, 149 (1984); S. M. Hedrick, E. A. Nielsen, J. Kavaler, D. I. Cohen, M. M. Davis, ibid., p. 153; Y. Yangi et al., ibid., p. 145; Y. Chien et al., ibid. 312, 31 (1984).
7. H. Saito et al., Nature 312, 36 (1984) [cloning of 2C α chain]; S. M. Hedrick, D. I. Cohen, E. A. Nielsen, M. M. Davis, ibid. 308, 149 (1984); S. M. Hedrick, E. A. Nielsen, J. Kavaler, D. I. Cohen, M. M. Davis, ibid., p. 153; Y. Yangi et al., ibid., p. 145; Y. Chien et al., ibid. 312, 31 (1984).
8. H. Saito et al., Nature 312, 36 (1984) [cloning of 2C α chain]; S. M. Hedrick, D. I. Cohen, E. A. Nielsen, M. M. Davis, ibid. 308, 149 (1984); S. M. Hedrick, E. A. Nielsen, J. Kavaler, D. I. Cohen, M. M. Davis, ibid., p. 153; Y. Yangi et al., ibid., p. 145; Y. Chien et al., ibid. 312, 31 (1984).
9. H. Saito et al., Nature 312, 36 (1984) [cloning of 2C α chain]; S. M. Hedrick, D. I. Cohen, E. A. Nielsen, M. M. Davis, ibid. 308, 149 (1984); S. M. Hedrick, E. A. Nielsen, J. Kavaler, D. I. Cohen, M. M. Davis, ibid., p. 153; Y. Yangi et al., ibid., p. 145; Y. Chien et al., ibid. 312, 31 (1984).
10. M. M. Davis and P. J. Bjorkman, ibid. 334, 395 (1988)
11. S. Tonegawa, ibid. 302, 575 (1981); M. Kronenberg et al., Annu. Rev. Immunol. 4, 529 (1986).
12. S. Tonegawa, ibid. 302, 575 (1981); M. Kronenberg et al., Annu. Rev. Immunol. 4, 529 (1986).
13. P. Patten et al., Nature 312, 40 (1984).
14. D. R. Davies, E. A Padlan, S. Sheriff, Annu. Rev. Biochem. 59, 439 (1990); I. A. Wilson and R. L. Stanfield, Curr. Opin. Struct. Biol. 4, 857 (1994); I. A. Wilson et al., Methods Enzymol. 203, 153 (1991); I. A. Wilson et al., Ciba Found. Symp. 5, 139, (1991); E. A. Padlan, Mol. Immunol. 31, 169 (1994).
15. D. R. Davies, E. A Padlan, S. Sheriff, Annu. Rev. Biochem. 59, 439 (1990); I. A. Wilson and R. L. Stanfield, Curr. Opin. Struct. Biol. 4, 857 (1994); I. A. Wilson et al., Methods Enzymol. 203, 153 (1991); I. A. Wilson et al., Ciba Found. Symp. 5, 139, (1991); E. A. Padlan, Mol. Immunol. 31, 169 (1994).
16. D. R. Davies, E. A Padlan, S. Sheriff, Annu. Rev. Biochem. 59, 439 (1990); I. A. Wilson and R. L. Stanfield, Curr. Opin. Struct. Biol. 4, 857 (1994); I. A. Wilson et al., Methods Enzymol. 203, 153 (1991); I. A. Wilson et al., Ciba Found. Symp. 5, 139, (1991); E. A. Padlan, Mol. Immunol. 31, 169 (1994).
17. D. R. Davies, E. A Padlan, S. Sheriff, Annu. Rev. Biochem. 59, 439 (1990); I. A. Wilson and R. L. Stanfield, Curr. Opin. Struct. Biol. 4, 857 (1994); I. A. Wilson et al., Methods Enzymol. 203, 153 (1991); I. A. Wilson et al., Ciba Found. Symp. 5, 139, (1991); E. A. Padlan, Mol. Immunol. 31, 169 (1994).
18. D. R. Davies, E. A Padlan, S. Sheriff, Annu. Rev. Biochem. 59, 439 (1990); I. A. Wilson and R. L. Stanfield, Curr. Opin. Struct. Biol. 4, 857 (1994); I. A. Wilson et al., Methods Enzymol. 203, 153 (1991); I. A. Wilson et al., Ciba Found. Symp. 5, 139, (1991); E. A. Padlan, Mol. Immunol. 31, 169 (1994).
19. J. Novotny, S. Tonegawa, H. Saito, D. M. Kranz, H. N. Eisen, Proc. Natl. Acad. Sci. U.S.A. 83, 742 (1986).
20. C. Chothia, D. R. Bosswell, A. M. Lesk, EMBO J. 7, 3745 (1988).
21. L. M. Amzel and R. J. Poljak, Annu. Rev. Biochem. 48, 961 (1979).
22. I. Engel and S. M. Hedrick, Cell 54, 473 (1988); C. D. Katayama et al., EMBO J. 14, 927 (1995).
23. I. Engel and S. M. Hedrick, Cell 54, 473 (1988); C. D. Katayama et al., EMBO J. 14, 927 (1995).
24. J. L. Jorgensen et al., Nature 355, 224 (1992).
25. J.-M. Claverie, A. Prochnika-Chalufour, L. Bougueleret, Immunol. Today 10, 10 (1989).
26. D. B. Sant'Angelo et al., Immunity 4, 367 (1996).
27. G. A. Bentley, G. Boulot, K. Karjalainen, R. A. Mariuzza, Science 267, 1984 (1995).
28. B. A. Fields et al., ibid. 270, 1821 (1995). Coordinates for 1934.4 Vα were provided by R. A. Mariuzza. The Vα domain has an Ig-fold topology, but with an unexpected strand switch in which the c″ strand is H-bonded to the d strand of the outer β sheet, in contrast to the inner c′ strand, as in Ig variable domains.
29. Four distinct Ig structural subtypes have been defined on the basis of the number of strands and the spacing between c' and e strands; (i) c type, seven-stranded, as in C domains, with ∼21 amino acids spacing; (ii) v type, nine-stranded, as in V domains, with ∼25 amino acids spacing; (iii) s type, seven-stranded, strand-switched with ∼9 amino acids spacing; and (iv) h type, a hybrid between c and s types as described by P. Bork, L. Holm, and C. Sander [J. Mol. Biol. 242, 309 (1994)].
30. I. Engel, T. H. Ottenhoff, R. D. Klausner, Science 256, 1318 (1992); K. L. Hilyard et al., Proc. Natl. Acad. Sci. U.S.A. 91, 9057 (1994); Y. Reiter et al., Immunity 2, 281 (1995); W. F. Soo Hoo et al., Proc. Natl. Acad. Sci. U.S.A. 89, 4759 (1993); J. Novotny et al., ibid. 88, 8646 (1991).
31. I. Engel, T. H. Ottenhoff, R. D. Klausner, Science 256, 1318 (1992); K. L. Hilyard et al., Proc. Natl. Acad. Sci. U.S.A. 91, 9057 (1994); Y. Reiter et al., Immunity 2, 281 (1995); W. F. Soo Hoo et al., Proc. Natl. Acad. Sci. U.S.A. 89, 4759 (1993); J. Novotny et al., ibid. 88, 8646 (1991).
32. I. Engel, T. H. Ottenhoff, R. D. Klausner, Science 256, 1318 (1992); K. L. Hilyard et al., Proc. Natl. Acad. Sci. U.S.A. 91, 9057 (1994); Y. Reiter et al., Immunity 2, 281 (1995); W. F. Soo Hoo et al., Proc. Natl. Acad. Sci. U.S.A. 89, 4759 (1993); J. Novotny et al., ibid. 88, 8646 (1991).
33. I. Engel, T. H. Ottenhoff, R. D. Klausner, Science 256, 1318 (1992); K. L. Hilyard et al., Proc. Natl. Acad. Sci. U.S.A. 91, 9057 (1994); Y. Reiter et al., Immunity 2, 281 (1995); W. F. Soo Hoo et al., Proc. Natl. Acad. Sci. U.S.A. 89, 4759 (1993); J. Novotny et al., ibid. 88, 8646 (1991).
34. I. Engel, T. H. Ottenhoff, R. D. Klausner, Science 256, 1318 (1992); K. L. Hilyard et al., Proc. Natl. Acad. Sci. U.S.A. 91, 9057 (1994); Y. Reiter et al., Immunity 2, 281 (1995); W. F. Soo Hoo et al., Proc. Natl. Acad. Sci. U.S.A. 89, 4759 (1993); J. Novotny et al., ibid. 88, 8646 (1991).
35. S. Weber et al., Nature 356, 793 (1992); C. Gregoire et al., Proc. Natl. Acad. Sci. U.S.A. 88, 8077 (1991).
36. S. Weber et al., Nature 356, 793 (1992); C. Gregoire et al., Proc. Natl. Acad. Sci. U.S.A. 88, 8077 (1991).
37. A. Y. un et al., Science 249, 677 (1990).
38. S. Chung et al., Proc. Natl. Acad. Sci. U.S.A. 91, 12654 (1994).
39. H. C. Chang et al., ibid., p. 11408.
40. R. K. Strong et al., J. Immunol. 153, 4111 (1994).
41. E. S. Ward et al., Scand. J. Immunol. 34, 215 (1991).
42. W. C. Sha et al., Nature 335, 271 (1988).
43. d-p2Ca: Y. Sykulev et al., Immunity 1, 15 (1994); M. Corr et al., Science 265, 946 (1994).
44. d-p2Ca: Y. Sykulev et al., Immunity 1, 15 (1994); M. Corr et al., Science 265, 946 (1994).
45. d-p2Ca: Y. Sykulev et al., Immunity 1, 15 (1994); M. Corr et al., Science 265, 946 (1994).
46. d-p2Ca: Y. Sykulev et al., Immunity 1, 15 (1994); M. Corr et al., Science 265, 946 (1994).
47. M. R. Jackson, E. S. Song, Y. Yang, P. A. Peterson, Proc. Natl. Acad. Sci. U.S.A. 89, 12117 (1992); M. Matsumura et al., J. Biol. Chem. 267, 23589 (1992).
48. M. R. Jackson, E. S. Song, Y. Yang, P. A. Peterson, Proc. Natl. Acad. Sci. U.S.A. 89, 12117 (1992); M. Matsumura et al., J. Biol. Chem. 267, 23589 (1992).
49. b-dB/8 (26)], and the conformation-specific mAbs-clonotypic 1B2 [D. M. Kranz, S. Tonegawa, H. N. Eisen, Proc. Natl. Acad. Sci. U.S.A. 81, 7922 (1984)] and Vβ8-specific F23.1 [U. D. Stearz et al., J. Immunol. 134, 3994 (1985)].
50. b-dB/8 (26)], and the conformation-specific mAbs-clonotypic 1B2 [D. M. Kranz, S. Tonegawa, H. N. Eisen, Proc. Natl. Acad. Sci. U.S.A. 81, 7922 (1984)] and Vβ8-specific F23.1 [U. D. Stearz et al., J. Immunol. 134, 3994 (1985)].
51. For other TCRs expressed and purified in our laboratory, elimination or reduction of carbohydrate content has not so far been a successful strategy for improving crystal quality.
52. Although this crystal was initially assigned to the C2 space group (with ore molecule in the asymmetric unit), further examination of the data integraled as P2 (with two molecules in the asymmetric unit) revealed very weak but above background intensities for h + k = 2n + 1 reflections, which gradually increased at higher resolutions, an indication of strong pseudocentering of the cell.
53. m: B. W. Matthews, J. Mol. Biol. 33, 491 (1968); (ix) DENZO and SCALEPACK: Z. Otwinowski, in Data Collection and Processing, L. Sawyer, N. Isaacs, S. Bailey, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1993), p. 56; (x) PRO-CHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thornton, J. Appl. Crystallogr. 26, 283 (1983); (xi) 3D-PROFILE: R. Luthy et al., Nature 356, 83 (1992); and (xii) ERRAT: C. Colovos and T. O. Yeates, Protein Sci. 2, 1511 (1993).
54. m: B. W. Matthews, J. Mol. Biol. 33, 491 (1968); (ix) DENZO and SCALEPACK: Z. Otwinowski, in Data Collection and Processing, L. Sawyer, N. Isaacs, S. Bailey, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1993), p. 56; (x) PRO-CHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thornton, J. Appl. Crystallogr. 26, 283 (1983); (xi) 3D-PROFILE: R. Luthy et al., Nature 356, 83 (1992); and (xii) ERRAT: C. Colovos and T. O. Yeates, Protein Sci. 2, 1511 (1993).
55. m: B. W. Matthews, J. Mol. Biol. 33, 491 (1968); (ix) DENZO and SCALEPACK: Z. Otwinowski, in Data Collection and Processing, L. Sawyer, N. Isaacs, S. Bailey, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1993), p. 56; (x) PRO-CHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thornton, J. Appl. Crystallogr. 26, 283 (1983); (xi) 3D-PROFILE: R. Luthy et al., Nature 356, 83 (1992); and (xii) ERRAT: C. Colovos and T. O. Yeates, Protein Sci. 2, 1511 (1993).
56. m: B. W. Matthews, J. Mol. Biol. 33, 491 (1968); (ix) DENZO and SCALEPACK: Z. Otwinowski, in Data Collection and Processing, L. Sawyer, N. Isaacs, S. Bailey, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1993), p. 56; (x) PRO-CHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thornton, J. Appl. Crystallogr. 26, 283 (1983); (xi) 3D-PROFILE: R. Luthy et al., Nature 356, 83 (1992); and (xii) ERRAT: C. Colovos and T. O. Yeates, Protein Sci. 2, 1511 (1993).
57. m: B. W. Matthews, J. Mol. Biol. 33, 491 (1968); (ix) DENZO and SCALEPACK: Z. Otwinowski, in Data Collection and Processing, L. Sawyer, N. Isaacs, S. Bailey, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1993), p. 56; (x) PRO-CHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thornton, J. Appl. Crystallogr. 26, 283 (1983); (xi) 3D-PROFILE: R. Luthy et al., Nature 356, 83 (1992); and (xii) ERRAT: C. Colovos and T. O. Yeates, Protein Sci. 2, 1511 (1993).
58. m: B. W. Matthews, J. Mol. Biol. 33, 491 (1968); (ix) DENZO and SCALEPACK: Z. Otwinowski, in Data Collection and Processing, L. Sawyer, N. Isaacs, S. Bailey, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1993), p. 56; (x) PRO-CHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thornton, J. Appl. Crystallogr. 26, 283 (1983); (xi) 3D-PROFILE: R. Luthy et al., Nature 356, 83 (1992); and (xii) ERRAT: C. Colovos and T. O. Yeates, Protein Sci. 2, 1511 (1993).
59. m: B. W. Matthews, J. Mol. Biol. 33, 491 (1968); (ix) DENZO and SCALEPACK: Z. Otwinowski, in Data Collection and Processing, L. Sawyer, N. Isaacs, S. Bailey, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1993), p. 56; (x) PRO-CHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thornton, J. Appl. Crystallogr. 26, 283 (1983); (xi) 3D-PROFILE: R. Luthy et al., Nature 356, 83 (1992); and (xii) ERRAT: C. Colovos and T. O. Yeates, Protein Sci. 2, 1511 (1993).
60. m: B. W. Matthews, J. Mol. Biol. 33, 491 (1968); (ix) DENZO and SCALEPACK: Z. Otwinowski, in Data Collection and Processing, L. Sawyer, N. Isaacs, S. Bailey, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1993), p. 56; (x) PRO-CHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thornton, J. Appl. Crystallogr. 26, 283 (1983); (xi) 3D-PROFILE: R. Luthy et al., Nature 356, 83 (1992); and (xii) ERRAT: C. Colovos and T. O. Yeates, Protein Sci. 2, 1511 (1993).
61. m: B. W. Matthews, J. Mol. Biol. 33, 491 (1968); (ix) DENZO and SCALEPACK: Z. Otwinowski, in Data Collection and Processing, L. Sawyer, N. Isaacs, S. Bailey, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1993), p. 56; (x) PRO-CHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thornton, J. Appl. Crystallogr. 26, 283 (1983); (xi) 3D-PROFILE: R. Luthy et al., Nature 356, 83 (1992); and (xii) ERRAT: C. Colovos and T. O. Yeates, Protein Sci. 2, 1511 (1993).
62. m: B. W. Matthews, J. Mol. Biol. 33, 491 (1968); (ix) DENZO and SCALEPACK: Z. Otwinowski, in Data Collection and Processing, L. Sawyer, N. Isaacs, S. Bailey, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1993), p. 56; (x) PRO-CHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thornton, J. Appl. Crystallogr. 26, 283 (1983); (xi) 3D-PROFILE: R. Luthy et al., Nature 356, 83 (1992); and (xii) ERRAT: C. Colovos and T. O. Yeates, Protein Sci. 2, 1511 (1993).
63. m: B. W. Matthews, J. Mol. Biol. 33, 491 (1968); (ix) DENZO and SCALEPACK: Z. Otwinowski, in Data Collection and Processing, L. Sawyer, N. Isaacs, S. Bailey, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1993), p. 56; (x) PRO-CHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thornton, J. Appl. Crystallogr. 26, 283 (1983); (xi) 3D-PROFILE: R. Luthy et al., Nature 356, 83 (1992); and (xii) ERRAT: C. Colovos and T. O. Yeates, Protein Sci. 2, 1511 (1993).
64. m: B. W. Matthews, J. Mol. Biol. 33, 491 (1968); (ix) DENZO and SCALEPACK: Z. Otwinowski, in Data Collection and Processing, L. Sawyer, N. Isaacs, S. Bailey, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1993), p. 56; (x) PRO-CHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thornton, J. Appl. Crystallogr. 26, 283 (1983); (xi) 3D-PROFILE: R. Luthy et al., Nature 356, 83 (1992); and (xii) ERRAT: C. Colovos and T. O. Yeates, Protein Sci. 2, 1511 (1993).
65. m: B. W. Matthews, J. Mol. Biol. 33, 491 (1968); (ix) DENZO and SCALEPACK: Z. Otwinowski, in Data Collection and Processing, L. Sawyer, N. Isaacs, S. Bailey, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1993), p. 56; (x) PRO-CHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thornton, J. Appl. Crystallogr. 26, 283 (1983); (xi) 3D-PROFILE: R. Luthy et al., Nature 356, 83 (1992); and (xii) ERRAT: C. Colovos and T. O. Yeates, Protein Sci. 2, 1511 (1993).
66. m: B. W. Matthews, J. Mol. Biol. 33, 491 (1968); (ix) DENZO and SCALEPACK: Z. Otwinowski, in Data Collection and Processing, L. Sawyer, N. Isaacs, S. Bailey, Eds. (SERC Daresbury Laboratory, Warrington, UK, 1993), p. 56; (x) PRO-CHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thornton, J. Appl. Crystallogr. 26, 283 (1983); (xi) 3D-PROFILE: R. Luthy et al., Nature 356, 83 (1992); and (xii) ERRAT: C. Colovos and T. O. Yeates, Protein Sci. 2, 1511 (1993).
67. H3 domains. The entire constant region of Fab NC10 was disordered in the crystal structure of the NC10-neuraminadase complex [R. L. Malby et al., Structure 2, 733 (1994)].
68. H3 domains. The entire constant region of Fab NC10 was disordered in the crystal structure of the NC10-neuraminadase complex [R. L. Malby et al., Structure 2, 733 (1994)].
69. Cryocooling is not easily reproducible with the 2C crystals. After screening many cryoprotectants, we obtained moderate success by the gradual introduction of glycerol at a rate of 5 percent per hour to a final concentration of 25 percent. Still, this procedure most often resulted in corrupted diffraction patterns (split reflections, loss of resolution, smearing, or high mosaicity). Eventually, after more than 50 attempts with identical soaking and cryoconditions, one crystal was successfully frozen, which diffracted to higher resolution (2.45 Å versus 2.9 Å) with lower mosaicity (0.4°) than did room temperature crystals (0.6°).
70. α distance between the cysteine residues was appropriate for a disulfide bond, but its electron density was weak.
71. The NC41 Fab from an antibody to neuraminadase has a similar elbow angle of 148° [P. M. Colman et al., Nature 326, 358 (1987)].
72. α atoms that were used for overlaps of the individual TCR domains with antibodies (56).
73. α atoms that were used for overlaps of the individual TCR domains with antibodies (56).
74. J. H. Brown et al., Nature 364, 33 (1994).
75. K. C. Garcia et al., in preparation.
76. All TCR and Fab numbering in this article follow E. A. Kabat et al., Eds., Sequences of Proteins of Immunological Interest (National Institutes of Health, Bethesda, MD, ed. 5, 1991).
77. G. A. Bentley and R. A. Mariuzza, Annu. Rev. Immunol 14, 563 (1996).
78. With DALI, version 2.0, L. Holm and C. J. Sander, J. Mol. Biol. 233, 123 (1993).
79. Cβ residues 218 to 220 are involved in extensive van der Waals contacts with a symmetry-related molecule in the 2C crystal lattice.
80. Drosophila melanogaster cells are insect cells that correctly recognize N-linked glycosylation signals, Asn-X-Thr (Ser) [M. J. Fraser, In Vitro Cell. Dev. Biol. 25, 225 (1989)]. However, the N-linked oligosaccharide structures produced are usually smaller than those produced in mammalian cells [K. Kuroda et al., Virology 174, 418 (1990)]. The fucose moiety has an α1,6 linkage to the first GlcNAc that is directly connected to the side-chain amide nitrogen of the Asn-X-Ser (Thr) sequence. The carbohydrate content was estimated by mass spectrometry of glycosylated 20 (non-carboxypeptidase digested) and unglycosylated 2C (non-carboxypeptidase digested) prepared by inducing expression in the presence of tunicamycin (1 μg/ml). The glycosylated 2C was 58,829 daltons and the unglycosylated 2C was 53,965 daltons. On the assumption that each N-linked glycosylation site has 1 to 1.5 kD of carbohydrate, then only four or five possible N-linked sites are occupied. Alternatively, N-linked glycosylation may not have been completely inhibited.
81. Drosophila melanogaster cells are insect cells that correctly recognize N-linked glycosylation signals, Asn-X-Thr (Ser) [M. J. Fraser, In Vitro Cell. Dev. Biol. 25, 225 (1989)]. However, the N-linked oligosaccharide structures produced are usually smaller than those produced in mammalian cells [K. Kuroda et al., Virology 174, 418 (1990)]. The fucose moiety has an α1,6 linkage to the first GlcNAc that is directly connected to the side-chain amide nitrogen of the Asn-X-Ser (Thr) sequence. The carbohydrate content was estimated by mass spectrometry of glycosylated 20 (non-carboxypeptidase digested) and unglycosylated 2C (non-carboxypeptidase digested) prepared by inducing expression in the presence of tunicamycin (1 μg/ml). The glycosylated 2C was 58,829 daltons and the unglycosylated 2C was 53,965 daltons. On the assumption that each N-linked glycosylation site has 1 to 1.5 kD of carbohydrate, then only four or five possible N-linked sites are occupied. Alternatively, N-linked glycosylation may not have been completely inhibited.
82. 2, However, the density is clear and unambiguous (Fig. 1). The Cα domain has no crystal lattice packing interactions that probably contribute to the higher thermal parameters.
83. 2 of ∼180° [J. S. Richardson, Adv. Prot. Chem. 34, 167 (1981)].
84. The program DALI (41) was used to search for structurally similar proteins or domains among 642 structures in the Protein Data Bank. The highest Z scores (4.0 to 5.0, which are very low values) were obtained with Ig fold-containing molecules based on alignments with the back β sheet (and part of strand c) of the Cα (2.8 to 3.2 Å rms deviation over 68 to 71 residues). No reasonable alignments were found in which the top strands were included in the superposition.
85. K. P. Kearse et al., EMBO J. 13, 4504 (1994).
86. C. Geisler et al., J. Immunol. 148, 3469 (1992); S. Caspar-Bauguil et al., Scand J. Immunol. 40, 323 (1994).
87. C. Geisler et al., J. Immunol. 148, 3469 (1992); S. Caspar-Bauguil et al., Scand J. Immunol. 40, 323 (1994).
88. All molecular surface areas buried by interaction were calculated with the program MS [M. L. Connolly, J. Appl. Crystallogr. 16, 439 (1983)] with a 1.7 Å probe sphere and standard atomic radii, as described in (7)].
89. H(32 to 39, 105 to 112); and (vi) Vα (31 to 37, 103 to 108)-Vα (31 to 37, 103 to 108).
90. H3) domain. The additional rotation and translation required to optimize the β chain-H chain superposition describes the domain shift. This procedure is similar to that described in (35) with superpositions specified in (56).
91. Hydrogen bond interactions were based on both distance (3.5 Å cutoff) and geometrical considerations with HBPLUS [I. K. McDonald and J. M. Thornton, J. Mol. Biol. 238, 777 (1994)]. The van der Waals and salt-bridge interactions were calculated with the program CONTACSYM [S. Sheriff, W. A. Hendrickson, J. L. Smith, ibid. 197, 273 (1987)).
92. Hydrogen bond interactions were based on both distance (3.5 Å cutoff) and geometrical considerations with HBPLUS [I. K. McDonald and J. M. Thornton, J. Mol. Biol. 238, 777 (1994)]. The van der Waals and salt-bridge interactions were calculated with the program CONTACSYM [S. Sheriff, W. A. Hendrickson, J. L. Smith, ibid. 197, 273 (1987)).
93. L heterodimers from available Fab x-ray structures in the Protein Data Bank [F. C. Bernstein et al., J. Mol. Biol. 112, 535 (1977)] with the Vα-Vβ of 2C shows a range from an essentially identical domain-domain rotational relationship with many antibodies to up to 17° differences with others.
94. R. L Stanfield et al., Structure 1, 83 (1993).
95. P. M. Colman, Adv. Immunol. 43, 99 (1988).
96. L residues 113 to 117, 119, 132 to 136, 138, 140, 158 to 161, 163, 174 to 180, 193, 205, and 207 to 208, The Fabs in Fig. 7A were superimposed with 2C as described above and were F9. 13. 7 [J. Lescar, H. Souchen, P. Alzari, Protein Sci. 3, 788 (1994)]; D11.15 [V. Chitarra et al., Proc. Natl. Acad. Sci. U.S.A. 90, 7711 (1993)]; and CNJ206 [R. Zemel et al., Mol. Immunol 31, 127 (1994)].
97. L residues 113 to 117, 119, 132 to 136, 138, 140, 158 to 161, 163, 174 to 180, 193, 205, and 207 to 208, The Fabs in Fig. 7A were superimposed with 2C as described above and were F9. 13. 7 [J. Lescar, H. Souchen, P. Alzari, Protein Sci. 3, 788 (1994)]; D11.15 [V. Chitarra et al., Proc. Natl. Acad. Sci. U.S.A. 90, 7711 (1993)]; and CNJ206 [R. Zemel et al., Mol. Immunol 31, 127 (1994)].
98. L residues 113 to 117, 119, 132 to 136, 138, 140, 158 to 161, 163, 174 to 180, 193, 205, and 207 to 208, The Fabs in Fig. 7A were superimposed with 2C as described above and were F9. 13. 7 [J. Lescar, H. Souchen, P. Alzari, Protein Sci. 3, 788 (1994)]; D11.15 [V. Chitarra et al., Proc. Natl. Acad. Sci. U.S.A. 90, 7711 (1993)]; and CNJ206 [R. Zemel et al., Mol. Immunol 31, 127 (1994)].
99. L residues 113 to 117, 119, 132 to 136, 138, 140, 158 to 161, 163, 174 to 180, 193, 205, and 207 to 208, The Fabs in Fig. 7A were superimposed with 2C as described above and were F9. 13. 7 [J. Lescar, H. Souchen, P. Alzari, Protein Sci. 3, 788 (1994)]; D11.15 [V. Chitarra et al., Proc. Natl. Acad. Sci. U.S.A. 90, 7711 (1993)]; and CNJ206 [R. Zemel et al., Mol. Immunol 31, 127 (1994)].
100. L residues 113 to 117, 119, 132 to 136, 138, 140, 158 to 161, 163, 174 to 180, 193, 205, and 207 to 208, The Fabs in Fig. 7A were superimposed with 2C as described above and were F9. 13. 7 [J. Lescar, H. Souchen, P. Alzari, Protein Sci. 3, 788 (1994)]; D11.15 [V. Chitarra et al., Proc. Natl. Acad. Sci. U.S.A. 90, 7711 (1993)]; and CNJ206 [R. Zemel et al., Mol. Immunol 31, 127 (1994)].
101. L residues 113 to 117, 119, 132 to 136, 138, 140, 158 to 161, 163, 174 to 180, 193, 205, and 207 to 208, The Fabs in Fig. 7A were superimposed with 2C as described above and were F9. 13. 7 [J. Lescar, H. Souchen, P. Alzari, Protein Sci. 3, 788 (1994)]; D11.15 [V. Chitarra et al., Proc. Natl. Acad. Sci. U.S.A. 90, 7711 (1993)]; and CNJ206 [R. Zemel et al., Mol. Immunol 31, 127 (1994)].
102. L residues 113 to 117, 119, 132 to 136, 138, 140, 158 to 161, 163, 174 to 180, 193, 205, and 207 to 208, The Fabs in Fig. 7A were superimposed with 2C as described above and were F9. 13. 7 [J. Lescar, H. Souchen, P. Alzari, Protein Sci. 3, 788 (1994)]; D11.15 [V. Chitarra et al., Proc. Natl. Acad. Sci. U.S.A. 90, 7711 (1993)]; and CNJ206 [R. Zemel et al., Mol. Immunol 31, 127 (1994)].
103. L residues 113 to 117, 119, 132 to 136, 138, 140, 158 to 161, 163, 174 to 180, 193, 205, and 207 to 208, The Fabs in Fig. 7A were superimposed with 2C as described above and were F9. 13. 7 [J. Lescar, H. Souchen, P. Alzari, Protein Sci. 3, 788 (1994)]; D11.15 [V. Chitarra et al., Proc. Natl. Acad. Sci. U.S.A. 90, 7711 (1993)]; and CNJ206 [R. Zemel et al., Mol. Immunol 31, 127 (1994)].
104. L residues 113 to 117, 119, 132 to 136, 138, 140, 158 to 161, 163, 174 to 180, 193, 205,
105. L domains.
106. Y. Choi et al., Nature 346, 471 (1990) [Vβ interaction with superantigen]; A. V. Chernovsky et al., The 9th International Congress of Immunology, Abstract 2955 (Vα interaction with the accessory CD4].
107. Y. Choi et al., Nature 346, 471 (1990) [Vβ interaction with superantigen]; A. V. Chernovsky et al., The 9th International Congress of Immunology, Abstract 2955 (Vα interaction with the accessory CD4].
108. Despite the high degree of flexibility expected for a tetraglycine stretch of amino acids in a solvent exposed loop, the electron density for CDR3 is excellent. The Φ and ψ angles of CDR3β fall within accepted ranges for a classic gamma-type turn [J. S. Richardson, Adv. Protein Chem. 34, 167 (1981)].
109. C. Abergal and J-M. Claverie, Eur. J. Immunol. 21, 3021 (1991).
110. C. Chothia and A. M. Lesk, J. Mol. Biol. 196, 901 (1987); C. Chothia et al., Nature 342, 877 (1989).
111. C. Chothia and A. M. Lesk, J. Mol. Biol. 196, 901 (1987); C. Chothia et al., Nature 342, 877 (1989).
112. M. Schiffer, E. A. Kabat, T. T. Wu, Immunogenetics 35, 224 (1992).
113. Length was measured from the tip of CDR1α to CDR2β and width was measured from the furthest ends of CDR1α to CDR2α or CDR1β to CDR2β.
114. k system in [G. J. Kersh and P. M. Allen, J. Exp. Med., in press].
115. b-dEV8.
116. D. H. Fremont, E. A. Stura, M. Matsumura, P. A. Peterson, I. A. Wilson, Proc. Natl. Acad. Sci. U.S.A. 92, 2479 (1995).
117. K. C. Garcia, M. Degano, P. A. Peterson, L. Teyton, I. A. Wilson, unpublished data.
118. O. Epp et al., Eur. J. Biochem. 45, 513 (1974).
119. Graphics Programs: (i) The program TOM was compiled by Christian Cambillau (1987); (ii) AVS: C. Upson et al., IEEF Computer Graphics and Application 9, 30 (1989); (iii) MidasPlus 2.0: T. E. Ferrin, C. C. Huang, L. E. Jarvis, R. J Langridge, J. Mol. Graph. 6, 13 (1988); and (iv) POMS: M. L. Connolly, ibid. 11, 139 (1993).
120. Graphics Programs: (i) The program TOM was compiled by Christian Cambillau (1987); (ii) AVS: C. Upson et al., IEEF Computer Graphics and Application 9, 30 (1989); (iii) MidasPlus 2.0: T. E. Ferrin, C. C. Huang, L. E. Jarvis, R. J Langridge, J. Mol. Graph. 6, 13 (1988); and (iv) POMS: M. L. Connolly, ibid. 11, 139 (1993).
121. Graphics Programs: (i) The program TOM was compiled by Christian Cambillau (1987); (ii) AVS: C. Upson et al., IEEF Computer Graphics and Application 9, 30 (1989); (iii) MidasPlus 2.0: T. E. Ferrin, C. C. Huang, L. E. Jarvis, R. J Langridge, J. Mol. Graph. 6, 13 (1988); and (iv) POMS: M. L. Connolly, ibid. 11, 139 (1993).
122. We thank E. Stura for advice and help with data collection and heavy atom screening; T. Yeates, L. Pease, D Kranz, H. Eisen. C. Scott, and R. Stefanko for discussions, materials, and assistance; N. H. Xuong for use of the UCSD X-ray facility; R. Lerner for constant encouragement and support; and M. Pique for production of figures. Supported by NIH RO1 CA58896 (I.A.W.) and NIH postdoctoral training grant T32-A107244 (K.C.G.) This is publication 10295-M from The Scripps Research Institute. The coordinates for 2C have been deposited in the Protein Data Bank (Brookhaven National Laboratory, Upton, NY) with accession code 1TCR.