Journal
STRUCTURE
Volume 16, Issue 3, Pages 441-448Publisher
CELL PRESS
DOI: 10.1016/j.str.2008.02.007
Keywords
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Funding
- NCRR NIH HHS [P41RR02250] Funding Source: Medline
- NEI NIH HHS [PN2EY016525] Funding Source: Medline
- NIDDK NIH HHS [R01DK26758] Funding Source: Medline
- NIGMS NIH HHS [R01GM08139, R01 GM080139, R01 GM080139-02, P01GM064692] Funding Source: Medline
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In this work, we employ single-particle electron cryo-microscopy (cryo-EM) to reconstruct GroEL to similar to 4 angstrom 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 C alpha 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 alpha 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.
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