Structural basis of plasticity in T cell receptor recognition of a self peptide-MHC antigen

Science

Volumn 279, Issue 5354, 1998, Pages 1166-1172

  Garcia, K Christopher ^a   Degano, Massimo ^a   Pease, Larry R ^b   Huang, Mingdong ^a   Peterson, Per A ^c   Teyton, Luc ^a   Wilson, Ian A ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b MAYO CLINIC   (United States)

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

Author keywords

[No Author keywords available]

Indexed keywords

AUTOANTIGEN; MAJOR HISTOCOMPATIBILITY ANTIGEN; PEPTIDE; T LYMPHOCYTE RECEPTOR; T LYMPHOCYTE RECEPTOR BETA CHAIN;

ANTIGEN RECOGNITION; ARTICLE; COMPLEMENTARITY DETERMINING REGION; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; NONHUMAN; PLASTICITY; PRIORITY JOURNAL;

ANIMALS; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; H-2 ANTIGENS; LIGANDS; MICE; MICE, TRANSGENIC; MODELS, MOLECULAR; MUTATION; OLIGOPEPTIDES; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; RECEPTORS, ANTIGEN, T-CELL, ALPHA-BETA; RECOMBINANT PROTEINS;

EID: 0032549142     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.279.5354.1166     Document Type: Article

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49. free: A. T. Brünger, Nature 355, 472 (1992). (iii) Torsional dynamics: L. M. Rice and A. T. Brünger, Proteins 19(4), 277 (1994). CCP4: Collaborative Computational Project No. 4, Daresbury, UK (1994); Acta Cryst. D 50, 760 (1994). (v) O: T. A. Jones, J.-Y. Zou, S. W. Cowan, M. Kjeldgaard, Acta Cryst. A 47, 110 (1991). (vi) SIGMAA: R. J. Read, ibid. 42, 140 (1986). (vii) AMoRe: J. Navaza, ibid. 50, 157 (1994). (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. (viii) RAVE/MAMA: T. A. Jones, in Molecular Replacement, E. Dodson, Ed. (SERC Daresbury Laboratory, Warrington, UK, 1992), p. 91. (ix) PROCHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thortton, J. Appl. Cryst. 26, 283 (1983). (x) Rmsd's were calculated with PROFIT v.1.7 (A. C. R. Martin, SciTech Software, 1992-1996). Molecular surface areas buried by interaction were calculated with the program MS [M. L. Connolly, J. Appl. Crystallog. 16, 439 (1983)] by using a 1.7 Å probe sphere, 10-point spot density, and standard atomic radii, AVS: C. Upson, IEEE Comput. Graph. Appl. 9, 30 (1989). (xiii) PQMS: M. L. Connolly, J. Mol. Graph. 11, 139 (1993). (xiv) "Shake" omit maps: D. E. McRee, Practical Protein Crystallography (Academic Press, New York, 1993). (xv) Resolution estimate: G. J. Kleywegt and T. A. Jones, Acta Cryst. D 52, 826 (1996).
50. free: A. T. Brünger, Nature 355, 472 (1992). (iii) Torsional dynamics: L. M. Rice and A. T. Brünger, Proteins 19(4), 277 (1994). CCP4: Collaborative Computational Project No. 4, Daresbury, UK (1994); Acta Cryst. D 50, 760 (1994). (v) O: T. A. Jones, J.-Y. Zou, S. W. Cowan, M. Kjeldgaard, Acta Cryst. A 47, 110 (1991). (vi) SIGMAA: R. J. Read, ibid. 42, 140 (1986). (vii) AMoRe: J. Navaza, ibid. 50, 157 (1994). (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. (viii) RAVE/MAMA: T. A. Jones, in Molecular Replacement, E. Dodson, Ed. (SERC Daresbury Laboratory, Warrington, UK, 1992), p. 91. (ix) PROCHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thortton, J. Appl. Cryst. 26, 283 (1983). (x) Rmsd's were calculated with PROFIT v.1.7 (A. C. R. Martin, SciTech Software, 1992-1996). Molecular surface areas buried by interaction were calculated with the program MS [M. L. Connolly, J. Appl. Crystallog. 16, 439 (1983)] by using a 1.7 Å probe sphere, 10-point spot density, and standard atomic radii, AVS: C. Upson, IEEE Comput. Graph. Appl. 9, 30 (1989). (xiii) PQMS: M. L. Connolly, J. Mol. Graph. 11, 139 (1993). (xiv) "Shake" omit maps: D. E. McRee, Practical Protein Crystallography (Academic Press, New York, 1993). (xv) Resolution estimate: G. J. Kleywegt and T. A. Jones, Acta Cryst. D 52, 826 (1996).
51. free: A. T. Brünger, Nature 355, 472 (1992). (iii) Torsional dynamics: L. M. Rice and A. T. Brünger, Proteins 19(4), 277 (1994). CCP4: Collaborative Computational Project No. 4, Daresbury, UK (1994); Acta Cryst. D 50, 760 (1994). (v) O: T. A. Jones, J.-Y. Zou, S. W. Cowan, M. Kjeldgaard, Acta Cryst. A 47, 110 (1991). (vi) SIGMAA: R. J. Read, ibid. 42, 140 (1986). (vii) AMoRe: J. Navaza, ibid. 50, 157 (1994). (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. (viii) RAVE/MAMA: T. A. Jones, in Molecular Replacement, E. Dodson, Ed. (SERC Daresbury Laboratory, Warrington, UK, 1992), p. 91. (ix) PROCHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thortton, J. Appl. Cryst. 26, 283 (1983). (x) Rmsd's were calculated with PROFIT v.1.7 (A. C. R. Martin, SciTech Software, 1992-1996). Molecular surface areas buried by interaction were calculated with the program MS [M. L. Connolly, J. Appl. Crystallog. 16, 439 (1983)] by using a 1.7 Å probe sphere, 10-point spot density, and standard atomic radii, AVS: C. Upson, IEEE Comput. Graph. Appl. 9, 30 (1989). (xiii) PQMS: M. L. Connolly, J. Mol. Graph. 11, 139 (1993). (xiv) "Shake" omit maps: D. E. McRee, Practical Protein Crystallography (Academic Press, New York, 1993). (xv) Resolution estimate: G. J. Kleywegt and T. A. Jones, Acta Cryst. D 52, 826 (1996).
52. free: A. T. Brünger, Nature 355, 472 (1992). (iii) Torsional dynamics: L. M. Rice and A. T. Brünger, Proteins 19(4), 277 (1994). CCP4: Collaborative Computational Project No. 4, Daresbury, UK (1994); Acta Cryst. D 50, 760 (1994). (v) O: T. A. Jones, J.-Y. Zou, S. W. Cowan, M. Kjeldgaard, Acta Cryst. A 47, 110 (1991). (vi) SIGMAA: R. J. Read, ibid. 42, 140 (1986). (vii) AMoRe: J. Navaza, ibid. 50, 157 (1994). (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. (viii) RAVE/MAMA: T. A. Jones, in Molecular Replacement, E. Dodson, Ed. (SERC Daresbury Laboratory, Warrington, UK, 1992), p. 91. (ix) PROCHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thortton, J. Appl. Cryst. 26, 283 (1983). (x) Rmsd's were calculated with PROFIT v.1.7 (A. C. R. Martin, SciTech Software, 1992-1996). Molecular surface areas buried by interaction were calculated with the program MS [M. L. Connolly, J. Appl. Crystallog. 16, 439 (1983)] by using a 1.7 Å probe sphere, 10-point spot density, and standard atomic radii, AVS: C. Upson, IEEE Comput. Graph. Appl. 9, 30 (1989). (xiii) PQMS: M. L. Connolly, J. Mol. Graph. 11, 139 (1993). (xiv) "Shake" omit maps: D. E. McRee, Practical Protein Crystallography (Academic Press, New York, 1993). (xv) Resolution estimate: G. J. Kleywegt and T. A. Jones, Acta Cryst. D 52, 826 (1996).
53. free: A. T. Brünger, Nature 355, 472 (1992). (iii) Torsional dynamics: L. M. Rice and A. T. Brünger, Proteins 19(4), 277 (1994). CCP4: Collaborative Computational Project No. 4, Daresbury, UK (1994); Acta Cryst. D 50, 760 (1994). (v) O: T. A. Jones, J.-Y. Zou, S. W. Cowan, M. Kjeldgaard, Acta Cryst. A 47, 110 (1991). (vi) SIGMAA: R. J. Read, ibid. 42, 140 (1986). (vii) AMoRe: J. Navaza, ibid. 50, 157 (1994). (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. (viii) RAVE/MAMA: T. A. Jones, in Molecular Replacement, E. Dodson, Ed. (SERC Daresbury Laboratory, Warrington, UK, 1992), p. 91. (ix) PROCHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thortton, J. Appl. Cryst. 26, 283 (1983). (x) Rmsd's were calculated with PROFIT v.1.7 (A. C. R. Martin, SciTech Software, 1992-1996). Molecular surface areas buried by interaction were calculated with the program MS [M. L. Connolly, J. Appl. Crystallog. 16, 439 (1983)] by using a 1.7 Å probe sphere, 10-point spot density, and standard atomic radii, AVS: C. Upson, IEEE Comput. Graph. Appl. 9, 30 (1989). (xiii) PQMS: M. L. Connolly, J. Mol. Graph. 11, 139 (1993). (xiv) "Shake" omit maps: D. E. McRee, Practical Protein Crystallography (Academic Press, New York, 1993). (xv) Resolution estimate: G. J. Kleywegt and T. A. Jones, Acta Cryst. D 52, 826 (1996).
54. free: A. T. Brünger, Nature 355, 472 (1992). (iii) Torsional dynamics: L. M. Rice and A. T. Brünger, Proteins 19(4), 277 (1994). CCP4: Collaborative Computational Project No. 4, Daresbury, UK (1994); Acta Cryst. D 50, 760 (1994). (v) O: T. A. Jones, J.-Y. Zou, S. W. Cowan, M. Kjeldgaard, Acta Cryst. A 47, 110 (1991). (vi) SIGMAA: R. J. Read, ibid. 42, 140 (1986). (vii) AMoRe: J. Navaza, ibid. 50, 157 (1994). (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. (viii) RAVE/MAMA: T. A. Jones, in Molecular Replacement, E. Dodson, Ed. (SERC Daresbury Laboratory, Warrington, UK, 1992), p. 91. (ix) PROCHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thortton, J. Appl. Cryst. 26, 283 (1983). (x) Rmsd's were calculated with PROFIT v.1.7 (A. C. R. Martin, SciTech Software, 1992-1996). Molecular surface areas buried by interaction were calculated with the program MS [M. L. Connolly, J. Appl. Crystallog. 16, 439 (1983)] by using a 1.7 Å probe sphere, 10-point spot density, and standard atomic radii, AVS: C. Upson, IEEE Comput. Graph. Appl. 9, 30 (1989). (xiii) PQMS: M. L. Connolly, J. Mol. Graph. 11, 139 (1993). (xiv) "Shake" omit maps: D. E. McRee, Practical Protein Crystallography (Academic Press, New York, 1993). (xv) Resolution estimate: G. J. Kleywegt and T. A. Jones, Acta Cryst. D 52, 826 (1996).
55. free: A. T. Brünger, Nature 355, 472 (1992). (iii) Torsional dynamics: L. M. Rice and A. T. Brünger, Proteins 19(4), 277 (1994). CCP4: Collaborative Computational Project No. 4, Daresbury, UK (1994); Acta Cryst. D 50, 760 (1994). (v) O: T. A. Jones, J.-Y. Zou, S. W. Cowan, M. Kjeldgaard, Acta Cryst. A 47, 110 (1991). (vi) SIGMAA: R. J. Read, ibid. 42, 140 (1986). (vii) AMoRe: J. Navaza, ibid. 50, 157 (1994). (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. (viii) RAVE/MAMA: T. A. Jones, in Molecular Replacement, E. Dodson, Ed. (SERC Daresbury Laboratory, Warrington, UK, 1992), p. 91. (ix) PROCHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thortton, J. Appl. Cryst. 26, 283 (1983). (x) Rmsd's were calculated with PROFIT v.1.7 (A. C. R. Martin, SciTech Software, 1992-1996). Molecular surface areas buried by interaction were calculated with the program MS [M. L. Connolly, J. Appl. Crystallog. 16, 439 (1983)] by using a 1.7 Å probe sphere, 10-point spot density, and standard atomic radii, AVS: C. Upson, IEEE Comput. Graph. Appl. 9, 30 (1989). (xiii) PQMS: M. L. Connolly, J. Mol. Graph. 11, 139 (1993). (xiv) "Shake" omit maps: D. E. McRee, Practical Protein Crystallography (Academic Press, New York, 1993). (xv) Resolution estimate: G. J. Kleywegt and T. A. Jones, Acta Cryst. D 52, 826 (1996).
56. free: A. T. Brünger, Nature 355, 472 (1992). (iii) Torsional dynamics: L. M. Rice and A. T. Brünger, Proteins 19(4), 277 (1994). CCP4: Collaborative Computational Project No. 4, Daresbury, UK (1994); Acta Cryst. D 50, 760 (1994). (v) O: T. A. Jones, J.-Y. Zou, S. W. Cowan, M. Kjeldgaard, Acta Cryst. A 47, 110 (1991). (vi) SIGMAA: R. J. Read, ibid. 42, 140 (1986). (vii) AMoRe: J. Navaza, ibid. 50, 157 (1994). (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. (viii) RAVE/MAMA: T. A. Jones, in Molecular Replacement, E. Dodson, Ed. (SERC Daresbury Laboratory, Warrington, UK, 1992), p. 91. (ix) PROCHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thortton, J. Appl. Cryst. 26, 283 (1983). (x) Rmsd's were calculated with PROFIT v.1.7 (A. C. R. Martin, SciTech Software, 1992-1996). Molecular surface areas buried by interaction were calculated with the program MS [M. L. Connolly, J. Appl. Crystallog. 16, 439 (1983)] by using a 1.7 Å probe sphere, 10-point spot density, and standard atomic radii, AVS: C. Upson, IEEE Comput. Graph. Appl. 9, 30 (1989). (xiii) PQMS: M. L. Connolly, J. Mol. Graph. 11, 139 (1993). (xiv) "Shake" omit maps: D. E. McRee, Practical Protein Crystallography (Academic Press, New York, 1993). (xv) Resolution estimate: G. J. Kleywegt and T. A. Jones, Acta Cryst. D 52, 826 (1996).
57. free: A. T. Brünger, Nature 355, 472 (1992). (iii) Torsional dynamics: L. M. Rice and A. T. Brünger, Proteins 19(4), 277 (1994). CCP4: Collaborative Computational Project No. 4, Daresbury, UK (1994); Acta Cryst. D 50, 760 (1994). (v) O: T. A. Jones, J.-Y. Zou, S. W. Cowan, M. Kjeldgaard, Acta Cryst. A 47, 110 (1991). (vi) SIGMAA: R. J. Read, ibid. 42, 140 (1986). (vii) AMoRe: J. Navaza, ibid. 50, 157 (1994). (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. (viii) RAVE/MAMA: T. A. Jones, in Molecular Replacement, E. Dodson, Ed. (SERC Daresbury Laboratory, Warrington, UK, 1992), p. 91. (ix) PROCHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thortton, J. Appl. Cryst. 26, 283 (1983). (x) Rmsd's were calculated with PROFIT v.1.7 (A. C. R. Martin, SciTech Software, 1992-1996). Molecular surface areas buried by interaction were calculated with the program MS [M. L. Connolly, J. Appl. Crystallog. 16, 439 (1983)] by using a 1.7 Å probe sphere, 10-point spot density, and standard atomic radii, AVS: C. Upson, IEEE Comput. Graph. Appl. 9, 30 (1989). (xiii) PQMS: M. L. Connolly, J. Mol. Graph. 11, 139 (1993). (xiv) "Shake" omit maps: D. E. McRee, Practical Protein Crystallography (Academic Press, New York, 1993). (xv) Resolution estimate: G. J. Kleywegt and T. A. Jones, Acta Cryst. D 52, 826 (1996).
58. free: A. T. Brünger, Nature 355, 472 (1992). (iii) Torsional dynamics: L. M. Rice and A. T. Brünger, Proteins 19(4), 277 (1994). CCP4: Collaborative Computational Project No. 4, Daresbury, UK (1994); Acta Cryst. D 50, 760 (1994). (v) O: T. A. Jones, J.-Y. Zou, S. W. Cowan, M. Kjeldgaard, Acta Cryst. A 47, 110 (1991). (vi) SIGMAA: R. J. Read, ibid. 42, 140 (1986). (vii) AMoRe: J. Navaza, ibid. 50, 157 (1994). (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. (viii) RAVE/MAMA: T. A. Jones, in Molecular Replacement, E. Dodson, Ed. (SERC Daresbury Laboratory, Warrington, UK, 1992), p. 91. (ix) PROCHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thortton, J. Appl. Cryst. 26, 283 (1983). (x) Rmsd's were calculated with PROFIT v.1.7 (A. C. R. Martin, SciTech Software, 1992-1996). Molecular surface areas buried by interaction were calculated with the program MS [M. L. Connolly, J. Appl. Crystallog. 16, 439 (1983)] by using a 1.7 Å probe sphere, 10-point spot density, and standard atomic radii, AVS: C. Upson, IEEE Comput. Graph. Appl. 9, 30 (1989). (xiii) PQMS: M. L. Connolly, J. Mol. Graph. 11, 139 (1993). (xiv) "Shake" omit maps: D. E. McRee, Practical Protein Crystallography (Academic Press, New York, 1993). (xv) Resolution estimate: G. J. Kleywegt and T. A. Jones, Acta Cryst. D 52, 826 (1996).
59. free: A. T. Brünger, Nature 355, 472 (1992). (iii) Torsional dynamics: L. M. Rice and A. T. Brünger, Proteins 19(4), 277 (1994). CCP4: Collaborative Computational Project No. 4, Daresbury, UK (1994); Acta Cryst. D 50, 760 (1994). (v) O: T. A. Jones, J.-Y. Zou, S. W. Cowan, M. Kjeldgaard, Acta Cryst. A 47, 110 (1991). (vi) SIGMAA: R. J. Read, ibid. 42, 140 (1986). (vii) AMoRe: J. Navaza, ibid. 50, 157 (1994). (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. (viii) RAVE/MAMA: T. A. Jones, in Molecular Replacement, E. Dodson, Ed. (SERC Daresbury Laboratory, Warrington, UK, 1992), p. 91. (ix) PROCHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thortton, J. Appl. Cryst. 26, 283 (1983). (x) Rmsd's were calculated with PROFIT v.1.7 (A. C. R. Martin, SciTech Software, 1992-1996). Molecular surface areas buried by interaction were calculated with the program MS [M. L. Connolly, J. Appl. Crystallog. 16, 439 (1983)] by using a 1.7 Å probe sphere, 10-point spot density, and standard atomic radii, AVS: C. Upson, IEEE Comput. Graph. Appl. 9, 30 (1989). (xiii) PQMS: M. L. Connolly, J. Mol. Graph. 11, 139 (1993). (xiv) "Shake" omit maps: D. E. McRee, Practical Protein Crystallography (Academic Press, New York, 1993). (xv) Resolution estimate: G. J. Kleywegt and T. A. Jones, Acta Cryst. D 52, 826 (1996).
60. free: A. T. Brünger, Nature 355, 472 (1992). (iii) Torsional dynamics: L. M. Rice and A. T. Brünger, Proteins 19(4), 277 (1994). CCP4: Collaborative Computational Project No. 4, Daresbury, UK (1994); Acta Cryst. D 50, 760 (1994). (v) O: T. A. Jones, J.-Y. Zou, S. W. Cowan, M. Kjeldgaard, Acta Cryst. A 47, 110 (1991). (vi) SIGMAA: R. J. Read, ibid. 42, 140 (1986). (vii) AMoRe: J. Navaza, ibid. 50, 157 (1994). (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. (viii) RAVE/MAMA: T. A. Jones, in Molecular Replacement, E. Dodson, Ed. (SERC Daresbury Laboratory, Warrington, UK, 1992), p. 91. (ix) PROCHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thortton, J. Appl. Cryst. 26, 283 (1983). (x) Rmsd's were calculated with PROFIT v.1.7 (A. C. R. Martin, SciTech Software, 1992-1996). Molecular surface areas buried by interaction were calculated with the program MS [M. L. Connolly, J. Appl. Crystallog. 16, 439 (1983)] by using a 1.7 Å probe sphere, 10-point spot density, and standard atomic radii, AVS: C. Upson, IEEE Comput. Graph. Appl. 9, 30 (1989). (xiii) PQMS: M. L. Connolly, J. Mol. Graph. 11, 139 (1993). (xiv) "Shake" omit maps: D. E. McRee, Practical Protein Crystallography (Academic Press, New York, 1993). (xv) Resolution estimate: G. J. Kleywegt and T. A. Jones, Acta Cryst. D 52, 826 (1996).
61. free: A. T. Brünger, Nature 355, 472 (1992). (iii) Torsional dynamics: L. M. Rice and A. T. Brünger, Proteins 19(4), 277 (1994). CCP4: Collaborative Computational Project No. 4, Daresbury, UK (1994); Acta Cryst. D 50, 760 (1994). (v) O: T. A. Jones, J.-Y. Zou, S. W. Cowan, M. Kjeldgaard, Acta Cryst. A 47, 110 (1991). (vi) SIGMAA: R. J. Read, ibid. 42, 140 (1986). (vii) AMoRe: J. Navaza, ibid. 50, 157 (1994). (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. (viii) RAVE/MAMA: T. A. Jones, in Molecular Replacement, E. Dodson, Ed. (SERC Daresbury Laboratory, Warrington, UK, 1992), p. 91. (ix) PROCHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thortton, J. Appl. Cryst. 26, 283 (1983). (x) Rmsd's were calculated with PROFIT v.1.7 (A. C. R. Martin, SciTech Software, 1992-1996). Molecular surface areas buried by interaction were calculated with the program MS [M. L. Connolly, J. Appl. Crystallog. 16, 439 (1983)] by using a 1.7 Å probe sphere, 10-point spot density, and standard atomic radii, AVS: C. Upson, IEEE Comput. Graph. Appl. 9, 30 (1989). (xiii) PQMS: M. L. Connolly, J. Mol. Graph. 11, 139 (1993). (xiv) "Shake" omit maps: D. E. McRee, Practical Protein Crystallography (Academic Press, New York, 1993). (xv) Resolution estimate: G. J. Kleywegt and T. A. Jones, Acta Cryst. D 52, 826 (1996).
62. free: A. T. Brünger, Nature 355, 472 (1992). (iii) Torsional dynamics: L. M. Rice and A. T. Brünger, Proteins 19(4), 277 (1994). CCP4: Collaborative Computational Project No. 4, Daresbury, UK (1994); Acta Cryst. D 50, 760 (1994). (v) O: T. A. Jones, J.-Y. Zou, S. W. Cowan, M. Kjeldgaard, Acta Cryst. A 47, 110 (1991). (vi) SIGMAA: R. J. Read, ibid. 42, 140 (1986). (vii) AMoRe: J. Navaza, ibid. 50, 157 (1994). (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. (viii) RAVE/MAMA: T. A. Jones, in Molecular Replacement, E. Dodson, Ed. (SERC Daresbury Laboratory, Warrington, UK, 1992), p. 91. (ix) PROCHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thortton, J. Appl. Cryst. 26, 283 (1983). (x) Rmsd's were calculated with PROFIT v.1.7 (A. C. R. Martin, SciTech Software, 1992-1996). Molecular surface areas buried by interaction were calculated with the program MS [M. L. Connolly, J. Appl. Crystallog. 16, 439 (1983)] by using a 1.7 Å probe sphere, 10-point spot density, and standard atomic radii, AVS: C. Upson, IEEE Comput. Graph. Appl. 9, 30 (1989). (xiii) PQMS: M. L. Connolly, J. Mol. Graph. 11, 139 (1993). (xiv) "Shake" omit maps: D. E. McRee, Practical Protein Crystallography (Academic Press, New York, 1993). (xv) Resolution estimate: G. J. Kleywegt and T. A. Jones, Acta Cryst. D 52, 826 (1996).
63. free: A. T. Brünger, Nature 355, 472 (1992). (iii) Torsional dynamics: L. M. Rice and A. T. Brünger, Proteins 19(4), 277 (1994). CCP4: Collaborative Computational Project No. 4, Daresbury, UK (1994); Acta Cryst. D 50, 760 (1994). (v) O: T. A. Jones, J.-Y. Zou, S. W. Cowan, M. Kjeldgaard, Acta Cryst. A 47, 110 (1991). (vi) SIGMAA: R. J. Read, ibid. 42, 140 (1986). (vii) AMoRe: J. Navaza, ibid. 50, 157 (1994). (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. (viii) RAVE/MAMA: T. A. Jones, in Molecular Replacement, E. Dodson, Ed. (SERC Daresbury Laboratory, Warrington, UK, 1992), p. 91. (ix) PROCHECK: R. A. Laskowski, M. W. MacArthur, S. D. Moss, J. M. Thortton, J. Appl. Cryst. 26, 283 (1983). (x) Rmsd's were calculated with PROFIT v.1.7 (A. C. R. Martin, SciTech Software, 1992-1996). Molecular surface areas buried by interaction were calculated with the program MS [M. L. Connolly, J. Appl. Crystallog. 16, 439 (1983)] by using a 1.7 Å probe sphere, 10-point spot density, and standard atomic radii, AVS: C. Upson, IEEE Comput. Graph. Appl. 9, 30 (1989). (xiii) PQMS: M. L. Connolly, J. Mol. Graph. 11, 139 (1993). (xiv) "Shake" omit maps: D. E. McRee, Practical Protein Crystallography (Academic Press, New York, 1993). (xv) Resolution estimate: G. J. Kleywegt and T. A. Jones, Acta Cryst. D 52, 826 (1996).
64. α domains. Methods for pairwise comparisons, superpositions, and measurements of interdomain angles in TCRs and their comparison to antibodies have been described (15).
65. The noncrystallographic symmetry relating the two molecules in the asymmetric unit of this TCR-pMHC complex crystal is of questionable biological relevance. The two complexes are oriented in opposite directions, which would be difficult to achieve in vivo when considering the polarity of the interaction surface of the T cell when in contact with an antigen-presenting cell. However, the situation in the crystal cannot be extrapolated directly to the in vivo environment, where higher order oligomers are an integral step in the TCR signaling complex [R. N. Germain, Curr. Biol. 7, R640 (1997)].
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76. b-dEV8 interface gives a value of 0.45. The value calculated for A6-HLA-A2-Tax is 0.47. For comparison, antibody-antigen complexes (0.66 to 0.68) and protein oligomeric interfaces (0.68 to 0.75) give values indicating better shape complementarity. The weak interaction of a crystal lattice contact gives a value of 0.35. Thus, according to this measurement, the shape complementarity of the TCR-pMHC interfaces are both quite poor.
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94. C maps with the program O (25). The final model contains all protein residues as well as four N-linked carbohydrate moieties and 184 ordered water molecules. Scattering of the bulk solvent was accounted for by using a flat model.
95. Interatomic contacts were evaluated both on distance and geometrical considerations. Van der Waals (<4.5 Å) and hydrogen-bond (<3.5 Å) interactions were calculated with the program CONTACSYM [S. Sheriff, W. A. Hendrickson, J. L. Smith, J. Mol. Biol. 197, 273 (1987)]. The designation "polar" was assigned to hydrogen-bond interactions that were within proper hydrogen-bonding distance but whose geometry deviates from ideality [I. K. McDonald and J. M. Thornton, ibid. 238, 777 (1994)], possibly because of the atomic error inherent in 3.0 Å x-ray data.
96. Interatomic contacts were evaluated both on distance and geometrical considerations. Van der Waals (<4.5 Å) and hydrogen-bond (<3.5 Å) interactions were calculated with the program CONTACSYM [S. Sheriff, W. A. Hendrickson, J. L. Smith, J. Mol. Biol. 197, 273 (1987)]. The designation "polar" was assigned to hydrogen-bond interactions that were within proper hydrogen-bonding distance but whose geometry deviates from ideality [I. K. McDonald and J. M. Thornton, ibid. 238, 777 (1994)], possibly because of the atomic error inherent in 3.0 Å x-ray data.
97. b-dEV8 have been deposited in the Protein Data Bank (PDB) (accession number 2CKB).