High-resolution structure of the Shigella type-III secretion needle by solid-state NMR and cryo-electron microscopy

Jean-Philippe Demers, Birgit Habenstein, Antoine Loquet, Suresh Kumar Vasa, Karin Giller, Stefan Becker, David Baker, Adam Lange () and Nikolaos G. Sgourakis ()
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Jean-Philippe Demers: Max Planck Institute for Biophysical Chemistry
Birgit Habenstein: Max Planck Institute for Biophysical Chemistry
Antoine Loquet: Max Planck Institute for Biophysical Chemistry
Suresh Kumar Vasa: Max Planck Institute for Biophysical Chemistry
Karin Giller: Max Planck Institute for Biophysical Chemistry
Stefan Becker: Max Planck Institute for Biophysical Chemistry
David Baker: University of Washington
Adam Lange: Max Planck Institute for Biophysical Chemistry
Nikolaos G. Sgourakis: University of Washington

Nature Communications, 2014, vol. 5, issue 1, 1-12

Abstract: Abstract We introduce a general hybrid approach for determining the structures of supramolecular assemblies. Cryo-electron microscopy (cryo-EM) data define the overall envelope of the assembly and rigid-body orientation of the subunits while solid-state nuclear magnetic resonance (ssNMR) chemical shifts and distance constraints define the local secondary structure, protein fold and inter-subunit interactions. Finally, Rosetta structure calculations provide a general framework to integrate the different sources of structural information. Combining a 7.7-Å cryo-EM density map and 996 ssNMR distance constraints, the structure of the type-III secretion system needle of Shigella flexneri is determined to a precision of 0.4 Å. The calculated structures are cross-validated using an independent data set of 691 ssNMR constraints and scanning transmission electron microscopy measurements. The hybrid model resolves the conformation of the non-conserved N terminus, which occupies a protrusion in the cryo-EM density, and reveals conserved pore residues forming a continuous pattern of electrostatic interactions, thereby suggesting a mechanism for effector protein translocation.

Date: 2014
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DOI: 10.1038/ncomms5976

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