A Toolbox for ab initio 3-D reconstructions in single-particle electron microscopy

Neil R. Voss, Dmitry Lyumkis, Anchi Cheng, Pick Wei Lau, Anke Mulder, Gabriel C. Lander, Edward J. Brignole, Denis Fellmann, Christopher Irving, Erica L. Jacovetty, Albert Leung, James Pulokas, Joel D. Quispe, Hanspeter Winkler, Craig Yoshioka, Bridget Carragher, Clinton S. Potter

Research output: Contribution to journalArticle

36 Scopus citations

Abstract

Structure determination of a novel macromolecular complex via single-particle electron microscopy depends upon overcoming the challenge of establishing a reliable 3-D reconstruction using only 2-D images. There are a variety of strategies that deal with this issue, but not all of them are readily accessible and straightforward to use. We have developed a "toolbox" of ab initio reconstruction techniques that provide several options for calculating 3-D volumes in an easily managed and tightly controlled work-flow that adheres to standard conventions and formats. This toolbox is designed to streamline the reconstruction process by removing the necessity for bookkeeping, while facilitating transparent data transfer between different software packages. It currently includes procedures for calculating ab initio reconstructions via random or orthogonal tilt geometry, tomograms, and common lines, all of which have been tested using the 50S ribosomal subunit. Our goal is that the accessibility of multiple independent reconstruction algorithms via this toolbox will improve the ease with which models can be generated, and provide a means of evaluating the confidence and reliability of the final reconstructed map.

Original languageEnglish (US)
Pages (from-to)389-398
Number of pages10
JournalJournal of Structural Biology
Volume169
Issue number3
DOIs
StatePublished - Mar 2010

Keywords

  • 3-D reconstruction
  • 50S ribosomal subunit
  • Initial model
  • Single-particle analysis
  • Transmission electron microscopy (TEM)

ASJC Scopus subject areas

  • Structural Biology

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    Voss, N. R., Lyumkis, D., Cheng, A., Lau, P. W., Mulder, A., Lander, G. C., Brignole, E. J., Fellmann, D., Irving, C., Jacovetty, E. L., Leung, A., Pulokas, J., Quispe, J. D., Winkler, H., Yoshioka, C., Carragher, B., & Potter, C. S. (2010). A Toolbox for ab initio 3-D reconstructions in single-particle electron microscopy. Journal of Structural Biology, 169(3), 389-398. https://doi.org/10.1016/j.jsb.2009.12.005