Crystal structure of rhodocytin, a ligand for the platelet-activating receptor CLEC-2

Protein Science

Volumn 17, Issue 9, 2008, Pages 1611-1616

  Watson, Aleksandra A ^a   Eble, Johannes A ^b   O'Callaghan, Chris A ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY HOSPITAL FRANKFURT   (Germany)

Author keywords

Aggretin; C type lectin; CLEC 2; CLEC1b; Platelets; Rhodocytin; Thrombosis

Indexed keywords

LECTIN; LECTIN RECEPTOR; PROTEIN; RHODOCYTIN; SNAKE VENOM; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; CRYSTAL STRUCTURE; ELECTRICITY; HYDROPHILICITY; MOLECULAR DOCKING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN INTERACTION; PROTEIN STRUCTURE; THROMBOCYTE ACTIVATION; THROMBOCYTE AGGREGATION;

AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; BLOOD PLATELETS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; CRYSTALLIZATION; DIMERIZATION; DISULFIDES; HUMANS; HYDROPHOBICITY; LECTINS, C-TYPE; LIGANDS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR WEIGHT; PLATELET ACTIVATION; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEIN SUBUNITS; SEQUENCE HOMOLOGY, AMINO ACID; STATIC ELECTRICITY; VIPER VENOMS; X-RAY DIFFRACTION;

EID: 50049114142     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.035568.108     Document Type: Article

References (34)

1. Baker, N.A., Sept, D., Joseph, S., Holst, M.J., and McCammon, J.A. 2001. Electrostatics of nanosystems: Application to microtubules and the ribosome. Proc. Natl. Acad. Sci. 98: 10037-10041.
2. Barrett, C.P., Hall, B.A., and Noble, M.E. 2004. Dynamite: A simple way to gain insight into protein motions. Acta Crystallogr. D Biol. Crystallogr. 60: 2280-2287.
3. Batuwangala, T., Leduc, M., Gibbins, J.M., Bon, C., and Jones, E.Y. 2004. Structure of the snake-venom toxin convulxin. Acta Crystallogr. D Biol. Crystallogr. 60: 46-53.
4. Beteva, A., Cipriani, F., Cusack, S., Delageniere, S., Gabadinho, J., Gordon, E.J., Guijarro, M., Hall, D.R., Larsen, S., Launer, L., et al. 2006. High-throughput sample handling and data collection at synchrotrons: Embedding the ESRF into the high-throughput gene-to-structure pipeline. Acta Crystallogr. D Biol. Crystallogr. 62: 1162-1169.
5. Brown, J.H. 2006. Breaking symmetry in protein dimers: Designs and functions. Protein Sci. 15: 1-13.
6. Chippaux, J.P. 1998. Snake-bites: Appraisal of the global situation. Bull. World Health Organ. 76: 515-524.
7. Christou, C.M., Pearce, A.C., Watson, A.A., Mistry, A.R., Pollitt, A.Y., Fenton-May, A.E., Johnson, L.A., Jackson, D.G., Watson, S.P., and O'Callaghan, C.A. 2008. Renal cells activate the platelet receptor CLEC-2 through podoplanin. Biochem. J. 411: 133-140.
8. Comeau, S.R., Gatchell, D.W., Vajda, S., and Camacho, C.J. 2004. ClusPro: A fully automated algorithm for protein-protein docking. Nucleic Acids Res. 32: W96-W99. doi: 10.1093/nar/gkh354.
9. Eble, J.A., Beermann, B., Hinz, H.J., and Schmidt-Hederich, A. 2001. α2 β 1 integrin is not recognized by rhodocytin but is the specific, high affinity target of rhodocetin, an RGD-independent disintegrin and potent inhibitor of cell adhesion to collagen. J. Biol. Chem. 276: 12274-12284.
10. Emsley, P. and Cowtan, K. 2004. Coot: Model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60: 2126-2132.
11. Fraczkiewicz, R. and Braun, W. 1998. Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules. J. Comput. Chem. 19: 319-333.
12. Fukuda, K., Mizuno, H., Atoda, H., and Morita, T. 2000. Crystal structure of flavocetin-A, a platelet glycoprotein Ib-binding protein, reveals a novel cyclic tetramer of C-type lectin-like heterodimers. Biochemistry 39: 1915-1923.
13. Fuller, G.L., Williams, J.A., Tomlinson, M.G., Eble, J.A., Hanna, S.L., Pohlmann, S., Suzuki-Inoue, K., Ozaki, Y., Watson, S.P., and Pearce, A.C. 2007. The C-type lectin receptors CLEC-2 and Dectin-1, but not DC-SIGN, signal via a novel YXXL-dependent signaling cascade. J. Biol. Chem. 282: 12397-12409.
14. Hirotsu, S., Mizuno, H., Fukuda, K., Qi, M.C., Matsui, T., Hamako, J., Morita, T., and Titani, K. 2001. Crystal structure of bitiscetin, a von Willebrand factor-dependent platelet aggregation inducer. Biochemistry 40: 13592-13597.
15. Ho, M., Warrell, D.A., Looareesuwan, S., Phillips, R.E., Chanthavanich, P., Karbwang, J., Supanaranond, W., Viravan, C., Hutton, R.A., and Vejcho, S. 1986. Clinical significance of venom antigen levels in patients envenomed by the Malayan pit viper (Calloselasma rhodostoma). Am. J. Trop. Med. Hyg. 35: 579-587.
16. Humphrey, W., Dalke, A., and Schulten, K. 1996. VMD: Visual molecular dynamics. J. Mol. Graph. 14: 33-38.
17. Ji, T.H., Grossmann, M., and Ji, I. 1998. G protein-coupled receptors. I. Diversity of receptor-ligand interactions. J. Biol. Chem. 273: 17299-17302.
18. Kato, K., Furihata, K., Cheli, Y., Radis-Baptista, G., and Kunicki, T.J. 2006. Effect of multimer size and a natural dimorphism on the binding of convulxin to platelet glycoprotein (GP)VI. J. Thromb. Haemost. 4: 1107-1113.
19. Long, F., Vagin, A.A., Young, P., and Murshudov, G.N. 2008. BALBES: A molecular-replacement pipeline. Acta Crystallogr. D Biol. Crystallogr. 64: 125-132.
20. Merritt, E.A. and Murphy, M.E. 1994. Raster3D Version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 50: 869-873.
21. Mizuno, H., Fujimoto, Z., Atoda, H., and Morita, T. 2001. Crystal structure of an anticoagulant protein in complex with the Gla domain of factor X. Proc. Natl. Acad. Sci. 98: 7230-7234.
22. Mizuno, H., Fujimoto, Z., Koizumi, M., Kano, H., Atoda, H., and Morita, T. 1997. Structure of coagulation factors IX/X-binding protein, a heterodimer of C-type lectin domains. Nat. Struct. Biol. 4: 438-441.
23. Murshudov, G.N., Vagin, A.A., and Dodson, E.J. 1997. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53: 240-255.
24. Otwinowski, Z. and Minor, W. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276: 307-326.
25. Shin, Y. and Morita, T. 1998. Rhodocytin, a functional novel platelet agonist belonging to the heterodimeric C-type lectin family, induces platelet aggregation independently of glycoprotein Ib. Biochem. Biophys. Res. Commun. 245: 741-745.
26. Suzuki-Inoue, K., Fuller, G.L., Garcia, A., Eble, J.A., Pohlmann, S., Inoue, O., Gartner, T.K., Hughan, S.C., Pearce, A.C., Laing, G.D., et al. 2006. A novel Syk-dependent mechanism of platelet activation by the C-type lectin receptor CLEC-2. Blood 107: 542-549.
27. Suzuki-Inoue, K., Kato, Y., Inoue, O., Kaneko, M.K., Mishima, K., Yatomi, Y., Yamazaki, Y., Narimatsu, H., and Ozaki, Y. 2007. Involvement of the snake toxin receptor CLEC-2, in podoplanin-mediated platelet activation, by cancer cells. J. Biol. Chem. 282: 25993-26001.
28. Vriend, G. 1990. WHAT IF: A molecular modeling and drug design program. J. Mol. Graph. 8: 52-56.
29. Walter, T.S., Diprose, J.M., Mayo, C.J., Siebold, C., Pickford, M.G., Carter, L., Sutton, G.C., Berrow, N.S., Brown, J., Berry, I.M., et al. 2005. A procedure for setting up high-throughput nanolitre crystallization experiments. Crystallization workflow for initial screening, automated storage, imaging and optimization. Acta Crystallogr. D Biol. Crystallogr. 61: 651-657.
30. Wang, R., Kong, C., Kolatkar, P., and Chung, M.C. 2001. A novel dimer of a C-type lectin-like heterodimer from the venom of Calloselasma rhodostoma (Malayan pit viper). FEBS Lett. 508: 447-453.
31. Watson, A.A. and O'Callaghan, C.A. 2005. Crystallization and X-ray diffraction analysis of human CLEC-2. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 61: 1094-1096.
32. Watson, A.A., Brown, J., Harlos, K., Eble, J.A., Walter, T.S., and O'Callaghan, C.A. 2007. The crystal structure and mutational binding analysis of the extracellular domain of the platelet-activating receptor CLEC-2. J. Biol. Chem. 282: 3165-3172.
33. Winn, M.D., Isupov, M.N., and Murshudov, G.N. 2001. Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr. D Biol. Crystallogr. 57: 122-133.
34. Xie, J., Wu, T., Guo, L., Ruan, Y., Zhou, L., Zhu, H., Yun, X., Hong, Y., Jiang, J., Wen, Y., et al. 2008. Molecular characterization of two novel isoforms and a soluble form of mouse CLEC-2. Biochem. Biophys. Res. Commun. 371: 180-184.