Biomolecular NMR Assignments

, Volume 2, Issue 2, pp 135–138 | Cite as

NMR assignment of the nonstructural protein nsp3(1066–1181) from SARS-CoV

  • Pedro Serrano
  • Margaret A. Johnson
  • Amarnath Chatterjee
  • Bill Pedrini
  • Kurt WüthrichEmail author


Sequence-specific NMR assignments of the globular core comprising the residues 1066–1181 within the non-structural protein nsp3e from the SARS coronavirus have been obtained using triple-resonance NMR experiments with the uniformly [13C, 15N]-labeled protein. The backbone and side chain assignments are nearly complete, providing the basis for the ongoing NMR structure determination. A preliminary identification of regular secondary structures has been derived from the 13C chemical shifts.


Severe acute respiratory syndrome SARS coronavirus Nonstructural protein NMR structure determination 



We thank Jeremiah Joseph, Vanitha Subramanian, Benjamin W. Neuman, Michael J. Buchmeier, Raymond C. Stevens, and Peter Kuhn of the Consortium for Functional and Structural Proteomics of the SARS-CoV for providing us with samples of nsp3(1066–1226) for the initial NMR screening. This study was supported by the NIAID/NIH contract #HHSN266200400058C “Functional and Structural Proteomics of the SARS-CoV” to P. Kuhn and M. J. Buchmeier, and by the Joint Center for Structural Genomics through the NIH/NIGMS Grant #U54-GM074898. Additional support was obtained for P. S., M. A. J. and B. P. through fellowships from the Spanish Ministry of Science and Education, the Canadian Institutes of Health Research, and the Swiss National Science Foundation (fellowship PA00A-109047/1), respectively, and by the Skaggs Institute for Chemical Biology. Kurt Wüthrich is the Cecil H. and Ida M. Green Professor of Structural Biology at TSRI.


  1. Herrmann T, Güntert P, Wüthrich K (2002a) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319:209–227. doi: 10.1016/S0022-2836(02)00241-3 CrossRefGoogle Scholar
  2. Herrmann T, Güntert P, Wüthrich K (2002b) Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS. J Biomol NMR 24:171–189. doi: 10.1023/A:1021614115432 CrossRefGoogle Scholar
  3. Luginbühl P, Güntert P, Billeter M, Wüthrich K (1995) Statistical basis for the use of 13Cα chemical shifts in protein structure determination. J Magn Reson 109:229–233. doi: 10.1006/jmrb.1995.0016 CrossRefGoogle Scholar
  4. Metzler WJ, Constantine KL, Friedrichs MS, Bell AJ, Ernst EG, Lavoie TB, et al (1993) Characterization of the three-dimensional solution structure of human profilin: 1H, 13C, and 15N NMR assignments and global folding pattern. Biochemistry 32:13818–13829. doi: 10.1021/bi00213a010 CrossRefGoogle Scholar
  5. Pastore A, Saudek V (1990) The relationship between chemical shift and secondary structure in proteins. J Magn Reson 90:165–176Google Scholar
  6. Ratia K, Saikatendu KS, Santarsiero BD, Barretto N, Baker SC, Stevens RC, et al (2006) Severe acute respiratory syndrome coronavirus papain-like protease: structure of a viral deubiquitinating enzyme. Proc Natl Acad Sci USA 103:5717–5722. doi: 10.1073/pnas.0510851103 CrossRefADSGoogle Scholar
  7. Saikatendu KS, Joseph JS, Subramanian V, Clayton T, Griffith M, Moy K, et al (2005) Structural basis of severe acute respiratory syndrome coronavirus ADP-ribose-1′′-phosphate dephosphorylation by a conserved domain of nsp3. Structure 13:1665–1675. doi: 10.1016/j.str.2005.07.022 CrossRefGoogle Scholar
  8. Saito H (1986) Conformation-dependent 13C chemical shifts: a new means of conformational characterization as obtained by high-resolution solid-state 13C NMR. Magn Reson Chem 24:835–852. doi: 10.1002/mrc.1260241002 CrossRefGoogle Scholar
  9. Sattler M, Schleucher J, Griesinger C (1999) Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients. Prog Nucl Magn Reson Spectrosc 34:93–158. doi: 10.1016/S0079-6565(98)00025-9 CrossRefGoogle Scholar
  10. Serrano P, Johnson MA, Almeida MS, Horst R, Herrmann T, Joseph JS, et al (2007) NMR structure of the N-terminal domain of the nonstructural protein 3 from the SARS coronavirus. J Virol 81:12049–12060. doi: 10.1128/JVI.00969-07 CrossRefGoogle Scholar
  11. Snijder EJ, Bredeenbeck PJ, Dobbe JC, Thiel V, Ziebuhr J, Poon LL, et al (2003) Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage. J Mol Biol 331:991–1004. doi: 10.1016/S0022-2836(03)00865-9 CrossRefGoogle Scholar
  12. Spera S, Bax A (1991) Empirical correlation between protein backbone conformation and Cα and Cβ 13C nuclear magnetic resonance chemical shifts. J Am Chem Soc 113:5490–5492. doi: 10.1021/ja00014a071 CrossRefGoogle Scholar
  13. Wishart DS, Sykes BD (1994) The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data. J Biomol NMR 4:135–140. doi: 10.1007/BF00175245 CrossRefGoogle Scholar
  14. Wishart DS, Bigam CG, Yao J, Abildgaard F, Dyson HJ, Oldfield E, et al (1995) 1H, 13C and 15N chemical shift referencing in biomolecular NMR. J Biomol NMR 6:135–140. doi: 10.1007/BF00211777 CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Pedro Serrano
    • 1
  • Margaret A. Johnson
    • 1
  • Amarnath Chatterjee
    • 1
  • Bill Pedrini
    • 1
  • Kurt Wüthrich
    • 2
    Email author
  1. 1.Department of Molecular BiologyThe Scripps Research InstituteLa JollaUSA
  2. 2.Department of Molecular Biology and Skaggs Institute for Chemical BiologyThe Scripps Research InstituteLa JollaUSA

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