Crystal structure of hemolin: A horseshoe shape with implications for homophilic adhesion

Science

Volumn 281, Issue 5379, 1998, Pages 991-995

  Su, Xiao Dong ^a,d   Gastinel, Louis N ^a,e   Vaughn, Daniel E ^a,f   Faye, Ingrid ^b   Poon, Pak ^c   Bjorkman, Pamela J ^a  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^b STOCKHOLM UNIVERSITY   (Sweden)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d LUND UNIVERSITY   (Sweden)

^e Centre National de la Recherche Scientifique   (France)

^f Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

IMMUNOGLOBULIN;

ARTICLE; BACTERIAL INFECTION; BINDING SITE; CRYSTAL STRUCTURE; IMMUNITY; INFECTION RESISTANCE; INSECT; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

BACTERIA (MICROORGANISMS); INSECTA;

EID: 0032516658     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.281.5379.991     Document Type: Article

References (60)

1. H. G. Boman, Cell 65, 205 (1991); J. A. Hoffmann, J.-M. Reichhart, C. Hetru, Curr. Opin. Immunol. 8, 8 (1996); I. Faye and M. Kanost, in Molecular Mechanisms of Immune Responses in Insects, P. T. Brey and D. Hultmark, Eds. (Chapman & Hall, London, 1997).
2. H. G. Boman, Cell 65, 205 (1991); J. A. Hoffmann, J.-M. Reichhart, C. Hetru, Curr. Opin. Immunol. 8, 8 (1996); I. Faye and M. Kanost, in Molecular Mechanisms of Immune Responses in Insects, P. T. Brey and D. Hultmark, Eds. (Chapman & Hall, London, 1997).
3. H. G. Boman, Cell 65, 205 (1991); J. A. Hoffmann, J.-M. Reichhart, C. Hetru, Curr. Opin. Immunol. 8, 8 (1996); I. Faye and M. Kanost, in Molecular Mechanisms of Immune Responses in Insects, P. T. Brey and D. Hultmark, Eds. (Chapman & Hall, London, 1997).
4. K. Andersson and H. Steiner, Insect Biochem. 17, 133 (1987); N. E. Ladendorff and M. R. Kanost, Arch. Insect Biochem. Physiol. 15, 33 (1990).
5. K. Andersson and H. Steiner, Insect Biochem. 17, 133 (1987); N. E. Ladendorff and M. R. Kanost, Arch. Insect Biochem. Physiol. 15, 33 (1990).
6. References for protein sequences: H. cecropia: hemolin [S.-C. Sun, I. Lindström, H. C. Boman, I. Faye, O. Schmidt, Science 250, 1729 (1990)]; revised sequence [I. Lindstöm-Dinnetz, S.-C. Sun, I. Faye, Eur. J. Biochem. 230, 920 (1995)]; M. sexta hemolin sequence and inhibition of hemocyte aggregation experiments [ N. E. Ladendorff and M. R. Kanost, Arch. Insect Biochem. Physiol. 18, 285 (1991)]; Drosophila neuroglian [A. J. Bieber et al., Cell 59, 447 (1989)]; sexta neuroglian [C.-L. Chen, D. J. Lampe, H. M. Robertson, J. B. Nardi, Dev. Biol. 181, 1 (1997)]; and human L1 [M. Kobayashi, M. Miura, H. Asou, K. Uyemura, Biochim. Biophys. Acta 1090, 238 (1991)].
7. References for protein sequences: H. cecropia: hemolin [S.-C. Sun, I. Lindström, H. C. Boman, I. Faye, O. Schmidt, Science 250, 1729 (1990)]; revised sequence [I. Lindstöm-Dinnetz, S.-C. Sun, I. Faye, Eur. J. Biochem. 230, 920 (1995)]; M. sexta hemolin sequence and inhibition of hemocyte aggregation experiments [ N. E. Ladendorff and M. R. Kanost, Arch. Insect Biochem. Physiol. 18, 285 (1991)]; Drosophila neuroglian [A. J. Bieber et al., Cell 59, 447 (1989)]; sexta neuroglian [C.-L. Chen, D. J. Lampe, H. M. Robertson, J. B. Nardi, Dev. Biol. 181, 1 (1997)]; and human L1 [M. Kobayashi, M. Miura, H. Asou, K. Uyemura, Biochim. Biophys. Acta 1090, 238 (1991)].
8. References for protein sequences: H. cecropia: hemolin [S.-C. Sun, I. Lindström, H. C. Boman, I. Faye, O. Schmidt, Science 250, 1729 (1990)]; revised sequence [I. Lindstöm-Dinnetz, S.-C. Sun, I. Faye, Eur. J. Biochem. 230, 920 (1995)]; M. sexta hemolin sequence and inhibition of hemocyte aggregation experiments [ N. E. Ladendorff and M. R. Kanost, Arch. Insect Biochem. Physiol. 18, 285 (1991)]; Drosophila neuroglian [A. J. Bieber et al., Cell 59, 447 (1989)]; sexta neuroglian [C.-L. Chen, D. J. Lampe, H. M. Robertson, J. B. Nardi, Dev. Biol. 181, 1 (1997)]; and human L1 [M. Kobayashi, M. Miura, H. Asou, K. Uyemura, Biochim. Biophys. Acta 1090, 238 (1991)].
9. References for protein sequences: H. cecropia: hemolin [S.-C. Sun, I. Lindström, H. C. Boman, I. Faye, O. Schmidt, Science 250, 1729 (1990)]; revised sequence [I. Lindstöm-Dinnetz, S.-C. Sun, I. Faye, Eur. J. Biochem. 230, 920 (1995)]; M. sexta hemolin sequence and inhibition of hemocyte aggregation experiments [ N. E. Ladendorff and M. R. Kanost, Arch. Insect Biochem. Physiol. 18, 285 (1991)]; Drosophila neuroglian [A. J. Bieber et al., Cell 59, 447 (1989)]; sexta neuroglian [C.-L. Chen, D. J. Lampe, H. M. Robertson, J. B. Nardi, Dev. Biol. 181, 1 (1997)]; and human L1 [M. Kobayashi, M. Miura, H. Asou, K. Uyemura, Biochim. Biophys. Acta 1090, 238 (1991)].
10. References for protein sequences: H. cecropia: hemolin [S.-C. Sun, I. Lindström, H. C. Boman, I. Faye, O. Schmidt, Science 250, 1729 (1990)]; revised sequence [I. Lindstöm-Dinnetz, S.-C. Sun, I. Faye, Eur. J. Biochem. 230, 920 (1995)]; M. sexta hemolin sequence and inhibition of hemocyte aggregation experiments [ N. E. Ladendorff and M. R. Kanost, Arch. Insect Biochem. Physiol. 18, 285 (1991)]; Drosophila neuroglian [A. J. Bieber et al., Cell 59, 447 (1989)]; sexta neuroglian [C.-L. Chen, D. J. Lampe, H. M. Robertson, J. B. Nardi, Dev. Biol. 181, 1 (1997)]; and human L1 [M. Kobayashi, M. Miura, H. Asou, K. Uyemura, Biochim. Biophys. Acta 1090, 238 (1991)].
11. References for protein sequences: H. cecropia: hemolin [S.-C. Sun, I. Lindström, H. C. Boman, I. Faye, O. Schmidt, Science 250, 1729 (1990)]; revised sequence [I. Lindstöm-Dinnetz, S.-C. Sun, I. Faye, Eur. J. Biochem. 230, 920 (1995)]; M. sexta hemolin sequence and inhibition of hemocyte aggregation experiments [ N. E. Ladendorff and M. R. Kanost, Arch. Insect Biochem. Physiol. 18, 285 (1991)]; Drosophila neuroglian [A. J. Bieber et al., Cell 59, 447 (1989)]; sexta neuroglian [C.-L. Chen, D. J. Lampe, H. M. Robertson, J. B. Nardi, Dev. Biol. 181, 1 (1997)]; and human L1 [M. Kobayashi, M. Miura, H. Asou, K. Uyemura, Biochim. Biophys. Acta 1090, 238 (1991)].
12. M. Hortsch, Neuron 17, 587 (1996).
13. A. Bateman et al., EMBO J. 15, 6050 (1996).
14. A. L. Hughes, Immunogenetics 47, 283 (1998).
15. R. Bettencourt, H. Lanz-Mendoza, K. Roxström Lindquist, I. Faye, Eur. J. Biochem. 250, 630 (1997). Although adhesive activity mediated by L1 family members is calcium-independent, hemolin-mediated aggregation of microspheres requires calcium, suggesting that L1 proteins and hemolin mediate homophilic adhesion in response to different signals. This potentially important functional difference does not have profound structural implication, because calcium-binding sites comprise only a few residues (typically three to six) [ C. A. McPhalen, N. C. J. Strynadka, M. N. G. James, Adv. Protein Chem. 42, 77 (1991)].
16. R. Bettencourt, H. Lanz-Mendoza, K. Roxström Lindquist, I. Faye, Eur. J. Biochem. 250, 630 (1997). Although adhesive activity mediated by L1 family members is calcium-independent, hemolin-mediated aggregation of microspheres requires calcium, suggesting that L1 proteins and hemolin mediate homophilic adhesion in response to different signals. This potentially important functional difference does not have profound structural implication, because calcium-binding sites comprise only a few residues (typically three to six) [ C. A. McPhalen, N. C. J. Strynadka, M. N. G. James, Adv. Protein Chem. 42, 77 (1991)].
17. H. Lanz-Mendoza, R. Bettencourt, M. Fabbri, I. Faye, Cell. Immunol. 169, 47 (1996).
18. L. Zhao and M. R. Kanost, J. Insect Physiol. 42, 73 (1996).
19. S. Daffre and I. Faye, FEBS Lett. 408, 127 (1997).
20. 395; Fig. 2A), and the protein (Nrg-4D) was expressed using a bacutovirus expression system. Nrg-4D was purified from the supernatants of infected High 5 cells using nickel nitrilotriacetic acid (Ni-NTA) chromatography (Ni-NTA superflow; Qiagen) followed by gel filtration using a Superdex 200 fast protein liquid chromatography column (Pharmacia).
21. 265) in the revised hemolin sequence (3). Ramachandran plot statistics (Table 1) are as defined by G. J. Kleywegt and T. A. Jones [Structure 4, 1395 (1996)]. Molecular surface areas buried by interaction were calculated using X-PLOR with a 1.4 Å radius. Electrostatic calculations were done and Fig. 1B was made using GRASP [A. Nicholls, R. Bharadwaj, B. Honig, Biophys. J. 64, A166 (1993)]. Figures 1A and 2B were made using MOLSCRIPT [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991)] and RASTER-3D [E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D. 50, 869 (1994)].
22. 265) in the revised hemolin sequence (3). Ramachandran plot statistics (Table 1) are as defined by G. J. Kleywegt and T. A. Jones [Structure 4, 1395 (1996)]. Molecular surface areas buried by interaction were calculated using X-PLOR with a 1.4 Å radius. Electrostatic calculations were done and Fig. 1B was made using GRASP [A. Nicholls, R. Bharadwaj, B. Honig, Biophys. J. 64, A166 (1993)]. Figures 1A and 2B were made using MOLSCRIPT [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991)] and RASTER-3D [E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D. 50, 869 (1994)].
23. 265) in the revised hemolin sequence (3). Ramachandran plot statistics (Table 1) are as defined by G. J. Kleywegt and T. A. Jones [Structure 4, 1395 (1996)]. Molecular surface areas buried by interaction were calculated using X-PLOR with a 1.4 Å radius. Electrostatic calculations were done and Fig. 1B was made using GRASP [A. Nicholls, R. Bharadwaj, B. Honig, Biophys. J. 64, A166 (1993)]. Figures 1A and 2B were made using MOLSCRIPT [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991)] and RASTER-3D [E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D. 50, 869 (1994)].
24. 265) in the revised hemolin sequence (3). Ramachandran plot statistics (Table 1) are as defined by G. J. Kleywegt and T. A. Jones [Structure 4, 1395 (1996)]. Molecular surface areas buried by interaction were calculated using X-PLOR with a 1.4 Å radius. Electrostatic calculations were done and Fig. 1B was made using GRASP [A. Nicholls, R. Bharadwaj, B. Honig, Biophys. J. 64, A166 (1993)]. Figures 1A and 2B were made using MOLSCRIPT [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991)] and RASTER-3D [E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D. 50, 869 (1994)].
25. 265) in the revised hemolin sequence (3). Ramachandran plot statistics (Table 1) are as defined by G. J. Kleywegt and T. A. Jones [Structure 4, 1395 (1996)]. Molecular surface areas buried by interaction were calculated using X-PLOR with a 1.4 Å radius. Electrostatic calculations were done and Fig. 1B was made using GRASP [A. Nicholls, R. Bharadwaj, B. Honig, Biophys. J. 64, A166 (1993)]. Figures 1A and 2B were made using MOLSCRIPT [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991)] and RASTER-3D [E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D. 50, 869 (1994)].
26. 265) in the revised hemolin sequence (3). Ramachandran plot statistics (Table 1) are as defined by G. J. Kleywegt and T. A. Jones [Structure 4, 1395 (1996)]. Molecular surface areas buried by interaction were calculated using X-PLOR with a 1.4 Å radius. Electrostatic calculations were done and Fig. 1B was made using GRASP [A. Nicholls, R. Bharadwaj, B. Honig, Biophys. J. 64, A166 (1993)]. Figures 1A and 2B were made using MOLSCRIPT [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991)] and RASTER-3D [E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D. 50, 869 (1994)].
27. 265) in the revised hemolin sequence (3). Ramachandran plot statistics (Table 1) are as defined by G. J. Kleywegt and T. A. Jones [Structure 4, 1395 (1996)]. Molecular surface areas buried by interaction were calculated using X-PLOR with a 1.4 Å radius. Electrostatic calculations were done and Fig. 1B was made using GRASP [A. Nicholls, R. Bharadwaj, B. Honig, Biophys. J. 64, A166 (1993)]. Figures 1A and 2B were made using MOLSCRIPT [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991)] and RASTER-3D [E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D. 50, 869 (1994)].
28. 265) in the revised hemolin sequence (3). Ramachandran plot statistics (Table 1) are as defined by G. J. Kleywegt and T. A. Jones [Structure 4, 1395 (1996)]. Molecular surface areas buried by interaction were calculated using X-PLOR with a 1.4 Å radius. Electrostatic calculations were done and Fig. 1B was made using GRASP [A. Nicholls, R. Bharadwaj, B. Honig, Biophys. J. 64, A166 (1993)]. Figures 1A and 2B were made using MOLSCRIPT [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991)] and RASTER-3D [E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D. 50, 869 (1994)].
29. 265) in the revised hemolin sequence (3). Ramachandran plot statistics (Table 1) are as defined by G. J. Kleywegt and T. A. Jones [Structure 4, 1395 (1996)]. Molecular surface areas buried by interaction were calculated using X-PLOR with a 1.4 Å radius. Electrostatic calculations were done and Fig. 1B was made using GRASP [A. Nicholls, R. Bharadwaj, B. Honig, Biophys. J. 64, A166 (1993)]. Figures 1A and 2B were made using MOLSCRIPT [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991)] and RASTER-3D [E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D. 50, 869 (1994)].
30. 265) in the revised hemolin sequence (3). Ramachandran plot statistics (Table 1) are as defined by G. J. Kleywegt and T. A. Jones [Structure 4, 1395 (1996)]. Molecular surface areas buried by interaction were calculated using X-PLOR with a 1.4 Å radius. Electrostatic calculations were done and Fig. 1B was made using GRASP [A. Nicholls, R. Bharadwaj, B. Honig, Biophys. J. 64, A166 (1993)]. Figures 1A and 2B were made using MOLSCRIPT [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991)] and RASTER-3D [E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D. 50, 869 (1994)].
31. 265) in the revised hemolin sequence (3). Ramachandran plot statistics (Table 1) are as defined by G. J. Kleywegt and T. A. Jones [Structure 4, 1395 (1996)]. Molecular surface areas buried by interaction were calculated using X-PLOR with a 1.4 Å radius. Electrostatic calculations were done and Fig. 1B was made using GRASP [A. Nicholls, R. Bharadwaj, B. Honig, Biophys. J. 64, A166 (1993)]. Figures 1A and 2B were made using MOLSCRIPT [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991)] and RASTER-3D [E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D. 50, 869 (1994)].
32. 265) in the revised hemolin sequence (3). Ramachandran plot statistics (Table 1) are as defined by G. J. Kleywegt and T. A. Jones [Structure 4, 1395 (1996)]. Molecular surface areas buried by interaction were calculated using X-PLOR with a 1.4 Å radius. Electrostatic calculations were done and Fig. 1B was made using GRASP [A. Nicholls, R. Bharadwaj, B. Honig, Biophys. J. 64, A166 (1993)]. Figures 1A and 2B were made using MOLSCRIPT [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991)] and RASTER-3D [E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D. 50, 869 (1994)].
33. 265) in the revised hemolin sequence (3). Ramachandran plot statistics (Table 1) are as defined by G. J. Kleywegt and T. A. Jones [Structure 4, 1395 (1996)]. Molecular surface areas buried by interaction were calculated using X-PLOR with a 1.4 Å radius. Electrostatic calculations were done and Fig. 1B was made using GRASP [A. Nicholls, R. Bharadwaj, B. Honig, Biophys. J. 64, A166 (1993)]. Figures 1A and 2B were made using MOLSCRIPT [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991)] and RASTER-3D [E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D. 50, 869 (1994)].
34. 265) in the revised hemolin sequence (3). Ramachandran plot statistics (Table 1) are as defined by G. J. Kleywegt and T. A. Jones [Structure 4, 1395 (1996)]. Molecular surface areas buried by interaction were calculated using X-PLOR with a 1.4 Å radius. Electrostatic calculations were done and Fig. 1B was made using GRASP [A. Nicholls, R. Bharadwaj, B. Honig, Biophys. J. 64, A166 (1993)]. Figures 1A and 2B were made using MOLSCRIPT [P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991)] and RASTER-3D [E. A. Merritt and M. E. P. Murphy, Acta Crystallogr. D. 50, 869 (1994)].
35. The sharing of strand A between the GFC and BED faces of the hemolin domains is a feature of V-and I-set, rather than C2, domains, as predicted by recent structure-based sequence alignments that suggest that many domains previously classified as C2, such as the hemolin domains and the IgSF domains of many CAMs, are members of the newly recognized I-set family [ Y. Harpaz and C. Chothia, J. Mol. Biol. 238, 528 (1994); D. E. Vaughn and P. J. Bjorkman, Neuron 16, 261 (1996); C. Chothia and E. Y. Jones, Annu. Rev. Biochem. 66, 823 (1997)]. Each hemolin domain includes a disulfide bond linking strands B and F; all domains except D3 contain a tryptophan at the position of the "invariant" tryptophan in Ig-like domains (D3 has a tyrosine at this position).
36. The sharing of strand A between the GFC and BED faces of the hemolin domains is a feature of V-and I-set, rather than C2, domains, as predicted by recent structure-based sequence alignments that suggest that many domains previously classified as C2, such as the hemolin domains and the IgSF domains of many CAMs, are members of the newly recognized I-set family [ Y. Harpaz and C. Chothia, J. Mol. Biol. 238, 528 (1994); D. E. Vaughn and P. J. Bjorkman, Neuron 16, 261 (1996); C. Chothia and E. Y. Jones, Annu. Rev. Biochem. 66, 823 (1997)]. Each hemolin domain includes a disulfide bond linking strands B and F; all domains except D3 contain a tryptophan at the position of the "invariant" tryptophan in Ig-like domains (D3 has a tyrosine at this position).
37. The sharing of strand A between the GFC and BED faces of the hemolin domains is a feature of V-and I-set, rather than C2, domains, as predicted by recent structure-based sequence alignments that suggest that many domains previously classified as C2, such as the hemolin domains and the IgSF domains of many CAMs, are members of the newly recognized I-set family [ Y. Harpaz and C. Chothia, J. Mol. Biol. 238, 528 (1994); D. E. Vaughn and P. J. Bjorkman, Neuron 16, 261 (1996); C. Chothia and E. Y. Jones, Annu. Rev. Biochem. 66, 823 (1997)]. Each hemolin domain includes a disulfide bond linking strands B and F; all domains except D3 contain a tryptophan at the position of the "invariant" tryptophan in Ig-like domains (D3 has a tyrosine at this position).
38. R. R. Copley and R. R. Barton, J. Mol. Biol. 242, 321 (1994). Although the structural details of hemolin's interactions with LPS remain to be elucidated, hemolin's phosphate-binding site and its structure in general bear no resemblance to the structure of bactericidal/permeability-increasing protein (BPI), a mammalian LPS-binding protein [L. J. Beamer, S. F. Carroll. D. Eisenberg, Science 276, 1861 (1997)].
39. R. R. Copley and R. R. Barton, J. Mol. Biol. 242, 321 (1994). Although the structural details of hemolin's interactions with LPS remain to be elucidated, hemolin's phosphate-binding site and its structure in general bear no resemblance to the structure of bactericidal/permeability-increasing protein (BPI), a mammalian LPS-binding protein [L. J. Beamer, S. F. Carroll. D. Eisenberg, Science 276, 1861 (1997)].
40. ab (PDB code 1DBB), J. H. Arevalo, E. A. Stura, M. J. Taussigh, I. A. Wilson, J. Mol. Biol. 231, 103 (1993); VCAM-1 (PDB code 1VCA), E. Y. Jones et al., Nature 373, 539 (1995); CD2 (PDB code 1HNG), E. Y. Jones, S. J. Davis, A. F. Williams, K. Harlos, D. I. Stuart, ibid. 360, 232 (1992), and ovalbumin (PDB code 1OVA), P. E. Stein, A. G. W. Leslie, J. T. Finch, R. W. Carrell, J. Mol. Biol. 221, 941 (1991).
41. ab (PDB code 1DBB), J. H. Arevalo, E. A. Stura, M. J. Taussigh, I. A. Wilson, J. Mol. Biol. 231, 103 (1993); VCAM-1 (PDB code 1VCA), E. Y. Jones et al., Nature 373, 539 (1995); CD2 (PDB code 1HNG), E. Y. Jones, S. J. Davis, A. F. Williams, K. Harlos, D. I. Stuart, ibid. 360, 232 (1992), and ovalbumin (PDB code 1OVA), P. E. Stein, A. G. W. Leslie, J. T. Finch, R. W. Carrell, J. Mol. Biol. 221, 941 (1991).
42. ab (PDB code 1DBB), J. H. Arevalo, E. A. Stura, M. J. Taussigh, I. A. Wilson, J. Mol. Biol. 231, 103 (1993); VCAM-1 (PDB code 1VCA), E. Y. Jones et al., Nature 373, 539 (1995); CD2 (PDB code 1HNG), E. Y. Jones, S. J. Davis, A. F. Williams, K. Harlos, D. I. Stuart, ibid. 360, 232 (1992), and ovalbumin (PDB code 1OVA), P. E. Stein, A. G. W. Leslie, J. T. Finch, R. W. Carrell, J. Mol. Biol. 221, 941 (1991).
43. ab (PDB code 1DBB), J. H. Arevalo, E. A. Stura, M. J. Taussigh, I. A. Wilson, J. Mol. Biol. 231, 103 (1993); VCAM-1 (PDB code 1VCA), E. Y. Jones et al., Nature 373, 539 (1995); CD2 (PDB code 1HNG), E. Y. Jones, S. J. Davis, A. F. Williams, K. Harlos, D. I. Stuart, ibid. 360, 232 (1992), and ovalbumin (PDB code 1OVA), P. E. Stein, A. G. W. Leslie, J. T. Finch, R. W. Carrell, J. Mol. Biol. 221, 941 (1991).
44. ab (PDB code 1DBB), J. H. Arevalo, E. A. Stura, M. J. Taussigh, I. A. Wilson, J. Mol. Biol. 231, 103 (1993); VCAM-1 (PDB code 1VCA), E. Y. Jones et al., Nature 373, 539 (1995); CD2 (PDB code 1HNG), E. Y. Jones, S. J. Davis, A. F. Williams, K. Harlos, D. I. Stuart, ibid. 360, 232 (1992), and ovalbumin (PDB code 1OVA), P. E. Stein, A. G. W. Leslie, J. T. Finch, R. W. Carrell, J. Mol. Biol. 221, 941 (1991).
45. ab (PDB code 1DBB), J. H. Arevalo, E. A. Stura, M. J. Taussigh, I. A. Wilson, J. Mol. Biol. 231, 103 (1993); VCAM-1 (PDB code 1VCA), E. Y. Jones et al., Nature 373, 539 (1995); CD2 (PDB code 1HNG), E. Y. Jones, S. J. Davis, A. F. Williams, K. Harlos, D. I. Stuart, ibid. 360, 232 (1992), and ovalbumin (PDB code 1OVA), P. E. Stein, A. G. W. Leslie, J. T. Finch, R. W. Carrell, J. Mol. Biol. 221, 941 (1991).
46. ab (PDB code 1DBB), J. H. Arevalo, E. A. Stura, M. J. Taussigh, I. A. Wilson, J. Mol. Biol. 231, 103 (1993); VCAM-1 (PDB code 1VCA), E. Y. Jones et al., Nature 373, 539 (1995); CD2 (PDB code 1HNG), E. Y. Jones, S. J. Davis, A. F. Williams, K. Harlos, D. I. Stuart, ibid. 360, 232 (1992), and ovalbumin (PDB code 1OVA), P. E. Stein, A. G. W. Leslie, J. T. Finch, R. W. Carrell, J. Mol. Biol. 221, 941 (1991).
47. The threshold of sequence identity that guarantees 3D similarity was established as 30% [C. Chothia and A. M. Lesk, EMBO J. 5, 823 (1986)]. Length-dependent sequence identity thresholds are discussed by R. A. Abagyan and S. Batalov [J. Mol. Biol. 273, 355 (1997) and references therein]. By these criteria, the hemolin domains and their counterparts in neuroglian are guaranteed to fold into similar tertiary structures.
48. The threshold of sequence identity that guarantees 3D similarity was established as 30% [C. Chothia and A. M. Lesk, EMBO J. 5, 823 (1986)]. Length-dependent sequence identity thresholds are discussed by R. A. Abagyan and S. Batalov [J. Mol. Biol. 273, 355 (1997) and references therein]. By these criteria, the hemolin domains and their counterparts in neuroglian are guaranteed to fold into similar tertiary structures.
49. hemolin = 1.36.
50. G. Rutherford, Y.-m. E. Wang, A. J. Bieber, in preparation.
51. 2-terminal Ig-like domains adopt an elongated structure. However, from our analysis of the published images, half are compatible with a folded structure at both ends of the protein.
52. 2-terminal Ig-like domains adopt an elongated structure. However, from our analysis of the published images, half are compatible with a folded structure at both ends of the protein.
53. 2-terminal Ig-like domains adopt an elongated structure. However, from our analysis of the published images, half are compatible with a folded structure at both ends of the protein.
54. L. Shapiro et al., Nature 374, 327 (1995).
55. 2 of surface area) are related by an approximate two-fold axis (177° rotation, 0.4 Å translation). The resulting hemolin dimer packs in a parallel "side by side" arrangement rather than a "head to head" arrangement. Hemolin is monomeric at the concentrations used for equilibrium analytical ultracentrifugation and mass spectrometry (unpublished results), but could dimerize at higher concentrations.
56. M. J. Bennett, M. P. Schlunegger, D. Eisenberg, Protein Sci. 4, 2455 (1995).
57. X.-D. Su and T. O. Yeates, unpublished data.
58. Single-letter abbreviations for amino acid residues: A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg; S, Ser; T, Thr; V, Val; W, Trp; and Y, Tyr.
59. T. S. Ranheim, G. M. Edelman, B. A. Cunningham, Proc. Natl. Acad. Sci. U.S.A. 93, 4071 (1996).
60. We thank T. O. Yeates for help with the Dom_angle program, H. P. Erickson for valuable discussions about ultracentrifugation data, A. J. Bieber for communicating results before publication, the Caltech PPMAL for mass spectrometry analyses, P. M. Snow and I. Nangiana for help with protein expression, Q. R. Fan for the KIR coordinates, and M. J. Bennett, L. M. Sánchez, and A. J. Chirino for discussions and help with crystallographic software. Hemolin coordinates have been deposited in the PDB (1BIH).