Fe-S clusters, essential cofactors needed for the activity of many different enzymes, are assembled by conserved protein machineries inside bacteria and mitochondria. As the architecture of the human machinery remains undefined, we co-expressed in Escherichia coli the following four proteins involved in the initial step of Fe-S cluster synthesis: FXN42-210 (iron donor); [NFS1]·[ISD11] (sulfur donor); and ISCU (scaffold upon which new clusters are assembled). We purified a stable, active complex consisting of all four proteins with 1:1:1:1 stoichiometry. Using negative staining transmission EM and single particle analysis, we obtained a three-dimensional model of the complex with ∼14 Å resolution. Molecular dynamics flexible fitting of protein structures docked into the EM map of the model revealed a [FXN42-210]24·[NFS1]24·[ISD11]24·[ISCU]24 complex, consistent with the measured 1:1:1:1 stoichiometry of its four components. The complex structure fulfills distance constraints obtained from chemical cross-linking of the complex at multiple recurring interfaces, involving hydrogen bonds, salt bridges, or hydrophobic interactions between conserved residues. The complex consists of a central roughly cubic [FXN42-210]24·[ISCU]24 sub-complex with one symmetric ISCU trimer bound on top of one symmetric FXN42-210 trimer at each of its eight vertices. Binding of 12 [NFS1]2·[ISD11]2 sub-complexes to the surface results in a globular macromolecule with a diameter of ∼15 nm and creates 24 Fe-S cluster assembly centers. The organization of each center recapitulates a previously proposed conserved mechanism for sulfur donation from NFS1 to ISCU and reveals, for the first time, a path for iron donation from FXN42-210 to ISCU.
Bibliographical noteFunding Information:
This work was supported in part by National Institutes of Health Grant AG15709-19 from NIA (to G. I. and J. T.). We thank Drs. R. Hafner (Characterization Facility, College of Science and Engineering, University of Minnesota) and W. Zang (Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota) for training and assisting in performing transmission EM; B. Madden (Proteomics Core, Mayo Clinic, Rochester, MN) for MS/MS data collection; J. Charlesworth (Microscopy and Cell Analysis Core, Mayo Clinic, Rochester, MN) for technical help; and Dr. S. Ludtke (Baylor College of Medicine) and the EMAN2 Discussion List for helpful suggestions.
© 2016 by The American Society for Biochemistry and Molecular Biology, Inc.