Abstract
The availability of new and fast tools in structure determination has led to a more than exponential growth of the number of structures solved per year. It is therefore increasingly essential to assess the accuracy of the new structures by reliable approaches able to assist validation. Here, we discuss a specific example in which the use of different complementary techniques, which include Bayesian methods and small angle scattering, resulted essential for validating the two currently available structures of the Josephin domain of ataxin-3, a protein involved in the ubiquitin/proteasome pathway and responsible for neurodegenerative spinocerebellar ataxia of type 3. Taken together, our results demonstrate that only one of the two structures is compatible with the experimental information. Based on the high precision of our refined structure, we show that Josephin contains an open cleft which could be directly implicated in the interaction with polyubiquitin chains and other partners.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Bax A. (2003) Protein Sci., 12:1–16
Boulin C.J., Kempf R., Gabriel A., Koch M.H.J. (1988) Nucl. Instrum. Meth. A, 269:312–320
Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-unstleve R.W., et al. (1998) Acta Crystallog. Sect. D, 54:905–921
Burnett B., Li F., Pittman R.N. (2003) Hum. Mol. Genet., 12:3195–3205
Chai Y., Berke S.S., Cohen R.E., Paulson H.L. (2004) J. Biol. Chem., 279:3605–3611
Donaldson K.M., Li W., Ching K.A., Batalov S., Tsai C.C., Joazeiro C.A. (2003) Proc. Natl. Acad. Sci. USA, 100:8892–8897
Gabriel A., Dauvergne F. (1982) Nucl. Instrum. Meth., 201:223–224
Habeck M., Nilges M., Rieping W. (2005a) Phys. Rev. E. Stat. Nonlin. Soft Matter Phys., 72:031912
Habeck M., Nilges M., Rieping W. (2005b) Phys. Rev. Lett., 94:018105
Habeck M., Rieping W., Nilges M. (2006) Proc. Natl. Acad. Sci. USA, 103:1756–1761
Johnston S.C., Riddle S.M., Cohen R.E., Hill C.P. (1999) EMBO J., 18:3877–3887
Kawaguchi Y., Okamoto T., Taniwaki M., Aizawa M., Inoue M., Katayama S., Kawakami H., Nakamura S., Nishimura M., Akiguchi I., et al. (1994) Nat. Genet., 8:221–228
Koch M.H.J., Bordas J. (1983) Nucl. Instrum. Methods, 208:461–469
Konarev P.V., Volkov V.V., Sokolova A.V., Koch M.H.J., Svergun D.I. (2003) J. Appl. Crystallogr., 36:1277–1282
Kozin M.B., Svergun D.I. (2001) J. Appl. Crystallogr., 34:33–41
Laskowski R.A., Rullmannn J.A., MacArthur M.W., Kaptein R., Thornton J.M. (1996) J. Biomol. NMR, 8:477–486
Masino L, Nicastro G, Menon RP, Dal Piaz F, Calder L., Pastore A. (2004) J. Mol Biol., 344:1021–1035
Masino L., Musi V., Menon R.P., Fusi P., Kelly G., Frenkiel T.A., Trottier Y., Pastore A. (2003) FEBS Lett., 549:21–25
Mao Y., Senic-Matuglia F, Di Fiore P.P., Polo S., Hodsdon M.E., De Camilli P. (2005) Proc. Natl. Acad. Sci. USA, 102:12700–12705
Munishkina L.A., Cooper E.M., Uversky V.N., Fink A.L. (2004) J. Mol. Recognit., 17:456–464
Nicastro G., Menon R.P., Masino L, Knowles P.P., McDonald N.Q., Pastore A. (2005) Proc. Natl. Acad. Sci. USA, 102:10493–10498
Nicastro G., Masino L., Frenkiel T.A., Kelly G., McCormick J., Menon R.P., Pastore A. (2004) J. Biomol. NMR, 30:457–458
Porod, G. (1982) In Small-angle X-ray scattering, Glatter, O. and Kratky, O. (Eds.), Academic Press, London, pp. 17–51
Rieping W., Habeck M., Nilges M. (2005a) Science, 309:303–306
Rieping W., Habeck M., Nilges M. (2005b) J. Am. Chem. Soc., 127:16026–16027
Sass H.J., Musco G., Stahl S.J., Wingfield P.T., Grzesiek S. (2000) J. Biomol. NMR, 18:303–309
Svergun D.I. (1992) J. Appl. Crystallogr., 25:495–503
Svergun D.I. (1999) Biophys. J., 76:2879–2886
Svergun D.I., Koch M.H.J. (2003) Rep. Progr. Phys., 66:1735–1782
Svergun D.I., Barberato C., Koch M.H.J. (1995) J. Appl. Crystallogr., 28:768–773
Svergun D.I., Petoukhov M.V., M.H.J. Koch M.H.J. (2001) Biophys. J., 80:2946–2953
Taylor J.P., Hardy J., Fischbeck K.H. (2002) Science, 296:1991–1995
Vestergaard B., Sanyal S., Roessle M., Mora L., Buckingham R.H., Kastrup J.S., Gajhede M., Svergun D.I., Ehrenberg M. (2005) Mol. Cell, 20:929–938
Volkov V.V., Svergun D.I. (2003) J. Appl. Crystallogr., 36:860–864
Vriend G. (1990) J. Mol. Graph., 8:52–56
Acknowledgements
This work is supported by the EUROSCA European consortium.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Nicastro, G., Habeck, M., Masino, L. et al. Structure validation of the Josephin domain of ataxin-3: Conclusive evidence for an open conformation. J Biomol NMR 36, 267–277 (2006). https://doi.org/10.1007/s10858-006-9092-z
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10858-006-9092-z