Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Commentary
  • Published:

Questions about the structure of the botulinum neurotoxin B light chain in complex with a target peptide

Nature Structural Biology volume 8, pages 663–664 (2001)Cite this article

Hanson and Stevens1 recently reported the cocrystal structure of the botulinum neurotoxin B light chain in complex with a 38-residue target peptide of synaptobrevin II. Based on a careful examination of the published data, we have serious concerns about the strength of experimental evidence supporting the presence of the target peptide, and consequently the validity of inferences about substrate binding made in the report.

The experimental B-factors (PDB entry 1f83) are excessively high for the substrate atoms. Their average B-factor is 128 Å2, approximately four times the average B-factor for the protease atoms. While B-factors alone do not provide a definitive measure of quality for model features, excessive B-factors for the peptide substrate in this case raise warning signs.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Electron density for modeled substrate synaptobrevin II and BotB light chain.

References

  1. Hanson, M.A. & Stevens, R.C. Nature Struct. Biol. 7, 687–692 (2000).

    Article  CAS  Google Scholar 

  2. Uppsala electron density server. http://portray.bmc.uu.se/eds/

  3. Perrakis, A., Sixma, T.A., Wilson, K.S. & Lamzin, V.S. Acta Crystallogr. D 53, 448–445 (1997).

    Article  CAS  Google Scholar 

  4. Read, R.J. Acta Crystallogr. A 42, 140–149 (1986).

    Article  Google Scholar 

  5. Brünger, A.T. et al. Acta Crystallogr. D 54, 905–921 (1998).

    Article  Google Scholar 

  6. McRee, D.E. J. Mol. Graph. 10, 44–46 (1992).

    Article  Google Scholar 

  7. Sheldrick, G.M. & Schneider, T.R Methods Enzymol. 277, 319–343 (1997).

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Macromolecular Crystallography and Structural Genomics Group, Lawrence Livermore National Laboratory, Livermore, 94550, California, USA

    Bernhard Rupp & Brent Segelke

Authors
  1. Bernhard Rupp
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Brent Segelke
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Bernhard Rupp.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Rupp, B., Segelke, B. Questions about the structure of the botulinum neurotoxin B light chain in complex with a target peptide. Nat Struct Mol Biol 8, 663–664 (2001). https://doi.org/10.1038/90361

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/90361

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing