5KZ5

Architecture of the Human Mitochondrial Iron-Sulfur Cluster Assembly Machinery: the Complex Formed by the Iron Donor, the Sulfur Donor, and the Scaffold

Summary for 5KZ5

• Entry DOI: 10.2210/pdb5kz5/pdb
• EMDB information: 8293 8301
• Descriptor: Cysteine desulfurase, mitochondrial, Frataxin, mitochondrial, Iron-sulfur cluster assembly enzyme ISCU, mitochondrial (3 entities in total)
• Functional Keywords: frataxin, iron-sulfur protein, mitochondria, protein complex, transferase-oxidoreductase complex, transferase/oxidoreductase
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 36
• Total formula weight: 897651.04

Authors

Gakh, O.,Ranatunga, W.,Smith, D.Y.,Ahlgren, E.C.,Al-Karadaghi, S.,Thompson, J.R.,Isaya, G. (deposition date: 2016-07-22, release date: 2016-08-31, Last modification date: 2024-10-23)

Primary citation

Gakh, O.,Ranatunga, W.,Smith, D.Y.,Ahlgren, E.C.,Al-Karadaghi, S.,Thompson, J.R.,Isaya, G.
Architecture of the Human Mitochondrial Iron-Sulfur Cluster Assembly Machinery.
J.Biol.Chem., 291:21296-21321, 2016

PubMed Abstract: 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: FXN (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 [FXN]·[NFS1]·[ISD11]·[ISCU] 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 [FXN]·[ISCU] sub-complex with one symmetric ISCU trimer bound on top of one symmetric FXN trimer at each of its eight vertices. Binding of 12 [NFS1]·[ISD11] 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 FXN to ISCU.

PubMed: 27519411
DOI: 10.1074/jbc.M116.738542

Experimental method

ELECTRON MICROSCOPY (14.3 Å)