Crystal structure of the conserved core of HIV-1 Nef complexed with a Src family SH3 domain

Cell

Volumn 85, Issue 6, 1996, Pages 931-942

  Chi Hon, Lee ^b   Saksela, Kalle ^b   Mirza, Urooj A ^b   Chait, Brian T ^b   Kuriyan, John ^a  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

ISOLEUCINE; PROTEIN TYROSINE KINASE; VIRUS PROTEIN;

AMINO ACID SUBSTITUTION; ARTICLE; BINDING AFFINITY; CRYSTAL STRUCTURE; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS 1; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN ISOLATION; VIRUS MUTATION; VIRUS REPLICATION;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 0343494918     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(00)81276-3     Document Type: Article

References (40)

1. Bacon, D., and Anderson, W.F. (1988). A fast algorithm for rendering space-filling molecule pictures. J. Mol. Graph. 6, 219-220.
2. Bolen, J.B. (1993). Nonreceptor tyrosine protein kinases. Oncogene 8, 2025-2031.
3. Brünger, A.T. (1992). X-PLOR (Version 3.1), Manual (New Haven, Connecticut: The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University).
4. Brünger, A.T. (1993). Assessment of phase accuracy by cross validation: the free R value. Methods and applications. Acta Cryst. D49, 24-36.
5. Cohen, G.B., Ren, R., and Baltimore, D. (1995a). Modular binding domains in signal transduction proteins. Cell 80, 237-248.
6. Cohen, S.L., Ferre-D'Amare, A.R., Burley, S.K., and Chait, B.T. (1995b). Probing the solution structure of the DNA-binding protein Max by a combination of proteolysis and mass spectrometry. Protein Sci. 4, 1088-1099.
7. Daniel, M.D., Kirchoff, F., Czajak, S.C., Sehgal, P.K., and Derosiers, R.C. (1992). Protective effects of a live attenuated SIV vaccine with a deletion in the nef gene. Science 258, 1938-1941.
8. Deacon, N.J., Tsykin, A., Solomon, A., Smith, K., Ludford-Menting, M., Hooker, D.J., McPhee, D.A., Greenway, A.L., Ellett, A., Chatfield, C., Lawson, V.A., Crowe, S., Maerz, A., Sonza, S., Learmont, J., Sullivan, J.S., Cunningham, A., Dwyer, D., Dowton, D., and Mills, J. (1995). Genomic structure of an attenuated quasi species of HIV-1 from a blood transfusion donor and recipients. Science 270, 988-991.
9. Feng, S., Chen, J.K., Yu, H., Simon, J.A., and Schreiber, S.A. (1994). Two binding orientations for peptides to the Src SH3 domain: development of a general model for SH3-ligand interactions. Science 266, 1241-1247.
10. Feng, S., Kasahara, C., Rickles, R.J., and Schreiber, S.L. (1995). Specific interactions outside the proline-rich core of two classes of Src homology 3 ligands. Proc. Natl. Acad. Sci. USA 92, 12408-12415.
11. Freund, J., Kellner, R., Houthaeve, T., and Kalbitzer, H.R. (1994a). Stability and proteolytic domains of Nef protein from human immunodeficiency virus (HIV) type 1. Eur. J. Biochem. 227, 811-819.
12. Freund, J., Kellner, R., Konvalinka, J., Wolber, V., Kräusslich, H.-G., and Kalbitzer, H.R. (1994b). A possible regulation of negative factor (Nef) activity of human immunodeficiency virus type 1 by the viral protease. FEBS Lett. 223, 589-593.
13. Gosser, Y.Q., Zheng, J., Overduin, M., Mayer, B.J., and Cowburn, D. (1995). The solution structure of Abl SH3, and its relationship to SH2 in the SH(32) construct. Structure 3, 1075-1086.
14. Goudreau, N., Cornille, F., Duchesne, M., Parker, F., Tocqué, B., Garbay, C., and Roques, B.P. (1994). NMR structure of the N-terminal SH3 domain of GRB2 and its complex with a proline rich peptide from Sos. Nature Struct. Biol. 1, 898-907.
15. Grzesiek, S., Wingfield, P., Stahl, S., Kaufman, J.D., and Bax, A. (1995). Four-dimensional 15N-separated NOESY of slowly tumbling perdeuterated 15N-enriched proteins: applications to HIV-1 Nef. J. Am. Chem. Soc. 117, 9594-9595.
16. Grzesiek, S., Bax, A., Clore, G.M., Gronenborn, A.M., Hu, J.-S., Kaufman, J., Palmer, I., Stahl, S.J., and Wingfield, P.T. (1996). The solution structure of HIV-1 Nef reveals an unexpected fold and permits delineation of the binding surface for the SH3 domain of Hck tyrosine protein kinase. Nature Struct. Biol. 3, 340-345.
17. Hendrickson, W.A. (1991). Determination of macromolecular structures from anomalous diffraction of synchrotron data. Science 254, 51-58.
18. Huang, Y., Zhang, L., and Ho, D.D. (1995). Characterization of nef sequences in long-term survivors of human immunodeficiency virus type 1 infection. J. Virol. 69, 93-100.
19. Jones, T.A., Zou, J.Y., Cowan, S. W., and Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst. A47, 110-119.
20. Kestler, H.W., III, Ringler, D.J., Mori, K., Panicali, D.L., Sehgal, P.K., Daniel, M.D., and Desrosiers, R.C. (1991). Importance of the nef gene for maintenance of high virus loads and for development of AIDS. Cell 65, 651-662.
21. Kirchhoff, F., Greenough, T.C., Brettler, D.B., Sullivan, J.L., and Desrosiers, R.C. (1995). Absence of intact nef sequences in a long-term survivor with nonprogressive HIV-1 infection. N. Engl. J. Med. 332, 259-260.
22. Knudsen, B., Zheng, J., Feller, S.M., Mayer, J.P., Burrell, S.K., Cowburn, D., and Hanafusa, H. (1995). Affinity and specificity requirements for the first Src homology 3 domain of the Crk protein. EMBO J. 14, 2191-2198.
23. Kraulis, P. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24, 946-950.
24. Lee, C.-H., Leung, B., Lemmon, M.A., Zheng, J., Cowburn, D., Kuriyan, J., and Saksela, K. (1995). A single amino acid in the SH3 domain of Hck determines its high affinity and specificity in binding to HIV-1 Nef protein. EMBO J. 14, 5006-5015.
25. Lim, W.A., and Richards, F.M. (1994). Critical residues in an SH3 domain from Sem-5 suggest a mechanism for proline-rich peptide recognition. Nature Struct. Biol. 1, 221-225.
26. Lim, W.A., Richards, F.M., and Fox, R.O. (1994). Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains. Nature 372, 375-379.
27. Nicholls, A., Sharp, K.A., and Honig, B. (1991). Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281-296.
28. Noble, M.E.M., Musacchio, A., Saraste, M., Courtneidge, S.A., and Wierenga, R.K. (1993). Crystal structure of the SH3 domain in human Fyn: comparison of the three-dimensional structures of SH3 domains in tyrosine kinases and spectrin. EMBO J. 12, 2617-2624.
29. Pawson, T. (1995). Protein modules and signalling networks. Nature 373, 573-580.
30. Ren, R., Mayer, B.J., Cicchetti, P., and Baltimore, D. (1993). Identification of a ten-amino acid proline-rich SH3 binding site. Science 259, 1157-1161.
31. Saksela, K., Cheng, G., and Baltimore, D. (1995). Proline-rich (PxxP) motifs in HIV-1 Nef bind to SH3 domains of a subset of Src kinases and are required for the enhanced growth of Nef+ viruses but not for down-regulation of CD4. EMBO J. 14, 484-491.
32. Sawai, E.T., Baur, A., Struble, H., Peterlin, B.M., Levy, J. A., and Cheng-Mayer, C. (1994). Human immunodeficiency virus type I Nef associates with a cellular serine kinase in T lymphocytes. Proc. Natl. Acad. Sci. USA 91, 1539-1543.
33. Sawai, E.T., Baur, A.S., Peterlin, B.M., Levy, J.A., and Cheng-Mayer, C. (1995). A conserved domain and membrane targeting of Nef from HIV and SIV are required for association with a cellular serine kinase activity. J. Biol. Chem. 270, 15307-15314.
34. Shugars, D.C., Smith, M.S., Glueck, D.H., Nantermet, P.V., Seillier-Moiseiwitsch, F., and Swanstrom, R. (1993). Analysis of human immunodeficiency virus type 1 nef gene sequences present in vivo. J. Virol. 67, 4639-4650.
35. Terasawa, H., Kohda, D., Hatanaka, H., Tsuchiya, S., Ogura, K., Nagata, K., Ishii, S., Mandiyan, V., Ullrich, A., Schlessinger, J., and Inagaki, F. (1994). Structure of the N-terminal SH3 domain of GRB2 complexed with a peptide from the guanine nucleotide releasing factor Sos. Nature Struct. Biol. 1, 891-897.
36. Trono, D. (1995). HIV accessory proteins: leading roles for the supporting cast. Cell 82, 189-192.
37. Weis, W.I., Kahn, R., Fourme, R., Drickamer, K., and Hendrickson, W.A. (1991). Structure of the calcium-dependent lectin domain from a rat mannose-binding protein determined by MAD phasing. Science 254, 1608-1615.
38. Wu, X., Knudsen, B., Feller, S.M., Zheng, J., Sali, A., Cowburn, D., Hanafusa, H., and Kuriyan, J. (1995). Structural basis for the specific interaction of lysine-containing proline-rich peptides with the N-terminal SH3 domain of c-Crk. Structure 3, 215-226.
39. Yu, H., Chen, J.K., Feng, S., Dalgarno, D.C., Brauer, A.W., and Schreiber, S.L. (1994). Structural basis for the binding of proline-rich peptides to SH3 domains. Cell 76, 933-945.
40. Zhang, K.Y.J., and Main, P. (1990). The use of Sayre's equation with solvent flattening and histogram matching for phase extension and refinement of protein structures. Acta Cryst. A46, 377-381.