De Novo Backbone Trace of GroEL from Single Particle Electron Cryomicroscopy

Steven J. Ludtke, Matthew L. Baker, Dong Hua Chen, Jiu Li Song, David T. Chuang, Wah Chiu

Research output: Contribution to journalArticle

139 Scopus citations

Abstract

In this work, we employ single-particle electron cryo-microscopy (cryo-EM) to reconstruct GroEL to ∼4 Å resolution with both D7 and C7 symmetry. Using a newly developed skeletonization algorithm and secondary structure element identification in combination with sequence-based secondary structure prediction, we demonstrate that it is possible to achieve a de novo Cα trace directly from a cryo-EM reconstruction. The topology of our backbone trace is completely accurate, though subtle alterations illustrate significant differences from existing crystal structures. In the map with C7 symmetry, the seven monomers in each ring are identical; however, the subunits have a subtly different structure in each ring, particularly in the equatorial domain. These differences include an asymmetric salt bridge, density in the nucleotide-binding pocket of only one ring, and small shifts in α helix positions. This asymmetric conformation is different from previous asymmetric structures, including GroES-bound GroEL, and may represent a "primed state" in the chaperonin pathway.

Original languageEnglish (US)
Pages (from-to)441-448
Number of pages8
JournalStructure
Volume16
Issue number3
DOIs
StatePublished - Mar 11 2008

Keywords

  • PROTEINS

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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    Ludtke, S. J., Baker, M. L., Chen, D. H., Song, J. L., Chuang, D. T., & Chiu, W. (2008). De Novo Backbone Trace of GroEL from Single Particle Electron Cryomicroscopy. Structure, 16(3), 441-448. https://doi.org/10.1016/j.str.2008.02.007