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- PDB-5kz5: Architecture of the Human Mitochondrial Iron-Sulfur Cluster Assem... -

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Basic information

Entry
Database: PDB / ID: 5kz5
TitleArchitecture of the Human Mitochondrial Iron-Sulfur Cluster Assembly Machinery: the Complex Formed by the Iron Donor, the Sulfur Donor, and the Scaffold
Components
  • Cysteine desulfurase, mitochondrial
  • Frataxin, mitochondrial
  • Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
KeywordsTRANSFERASE/OXIDOREDUCTASE / frataxin / iron-sulfur protein / mitochondria / protein complex / TRANSFERASE-OXIDOREDUCTASE complex
Function / homology
Function and homology information


positive regulation of lyase activity / iron-sulfur cluster chaperone activity / negative regulation of iron ion import across plasma membrane / molybdopterin cofactor metabolic process / Molybdenum cofactor biosynthesis / proprioception / [4Fe-4S] cluster assembly / Mitochondrial iron-sulfur cluster biogenesis / sulfur carrier activity / Complex III assembly ...positive regulation of lyase activity / iron-sulfur cluster chaperone activity / negative regulation of iron ion import across plasma membrane / molybdopterin cofactor metabolic process / Molybdenum cofactor biosynthesis / proprioception / [4Fe-4S] cluster assembly / Mitochondrial iron-sulfur cluster biogenesis / sulfur carrier activity / Complex III assembly / iron chaperone activity / positive regulation of mitochondrial electron transport, NADH to ubiquinone / Maturation of TCA enzymes and regulation of TCA cycle / cysteine desulfurase / cysteine desulfurase activity / negative regulation of organ growth / Mo-molybdopterin cofactor biosynthetic process / mitochondrial respiratory chain complex III assembly / embryo development ending in birth or egg hatching / Mitochondrial protein import / iron-sulfur cluster assembly complex / mitochondrial [2Fe-2S] assembly complex / oxidative phosphorylation / response to iron ion / adult walking behavior / heme biosynthetic process / [2Fe-2S] cluster assembly / negative regulation of multicellular organism growth / organ growth / iron-sulfur cluster assembly / muscle cell cellular homeostasis / ferroxidase / negative regulation of release of cytochrome c from mitochondria / protein autoprocessing / ferroxidase activity / iron-sulfur cluster binding / ferric iron binding / protein maturation / iron ion transport / enzyme activator activity / ferrous iron binding / 2 iron, 2 sulfur cluster binding / cellular response to hydrogen peroxide / pyridoxal phosphate binding / Maturation of replicase proteins / molecular adaptor activity / intracellular iron ion homeostasis / iron ion binding / mitochondrial matrix / centrosome / negative regulation of apoptotic process / protein homodimerization activity / mitochondrion / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Frataxin / ISC system FeS cluster assembly, IscU scaffold / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Cysteine desulfurase IscS / NIF system FeS cluster assembly, NifU, N-terminal ...Frataxin / ISC system FeS cluster assembly, IscU scaffold / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Cysteine desulfurase IscS / NIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal domain / Frataxin/CyaY superfamily / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Frataxin, mitochondrial / Iron-sulfur cluster assembly enzyme ISCU / Cysteine desulfurase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 14.3 Å
AuthorsGakh, O. / Ranatunga, W. / Smith, D.Y. / Ahlgren, E.C. / Al-Karadaghi, S. / Thompson, J.R. / Isaya, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)AG15709-19 United States
CitationJournal: J Biol Chem / Year: 2016
Title: Architecture of the Human Mitochondrial Iron-Sulfur Cluster Assembly Machinery.
Authors: Oleksandr Gakh / Wasantha Ranatunga / Douglas Y Smith / Eva-Christina Ahlgren / Salam Al-Karadaghi / James R Thompson / Grazia Isaya /
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 ...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.
History
DepositionJul 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2May 3, 2017Group: Derived calculations
Revision 1.3Jul 18, 2018Group: Author supporting evidence / Data collection / Category: em_software / pdbx_audit_support
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _struct_sheet.number_strands

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Structure visualization

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Assembly

Deposited unit
1: Cysteine desulfurase, mitochondrial
2: Cysteine desulfurase, mitochondrial
3: Cysteine desulfurase, mitochondrial
4: Cysteine desulfurase, mitochondrial
M: Cysteine desulfurase, mitochondrial
N: Cysteine desulfurase, mitochondrial
O: Cysteine desulfurase, mitochondrial
P: Cysteine desulfurase, mitochondrial
Q: Cysteine desulfurase, mitochondrial
R: Cysteine desulfurase, mitochondrial
S: Cysteine desulfurase, mitochondrial
T: Cysteine desulfurase, mitochondrial
A: Frataxin, mitochondrial
a: Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
B: Frataxin, mitochondrial
b: Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
C: Frataxin, mitochondrial
c: Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
D: Frataxin, mitochondrial
d: Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
E: Frataxin, mitochondrial
e: Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
F: Frataxin, mitochondrial
f: Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
G: Frataxin, mitochondrial
g: Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
H: Frataxin, mitochondrial
h: Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
I: Frataxin, mitochondrial
i: Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
J: Frataxin, mitochondrial
j: Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
K: Frataxin, mitochondrial
k: Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
L: Frataxin, mitochondrial
l: Iron-sulfur cluster assembly enzyme ISCU, mitochondrial


Theoretical massNumber of molelcules
Total (without water)897,65136
Polymers897,65136
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area295710 Å2
ΔGint-1219 kcal/mol
Surface area202200 Å2

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Components

#1: Protein
Cysteine desulfurase, mitochondrial / NFS1


Mass: 43429.648 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFS1, NIFS, HUSSY-08 / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: Q9Y697, cysteine desulfurase
#2: Protein
Frataxin, mitochondrial / Friedreich ataxia protein / Fxn


Mass: 18849.025 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FXN, FRDA, X25 / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: Q16595, ferroxidase
#3: Protein
Iron-sulfur cluster assembly enzyme ISCU, mitochondrial / NifU-like N-terminal domain-containing protein / NifU-like protein / iron sulfur cluster scaffold protein


Mass: 12525.580 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ISCU, NIFUN / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: Q9H1K1
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: NFS1-ISD11-ISCU-FXN / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Plasmid: pCDF, pET
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris-HClC4H12ClNO31
2150 mMsodium chlorideNaCl1
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO / Details: 50 mM Tris-HCl, pH 8.0, 150 mM NaCl
EM stainingType: NEGATIVE / Details: 5 and 30 seconds / Material: 1% uranyl acetate
Specimen supportDetails: DV-502A vacuum evaporator (Denton Vacuum Inc.) / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Carbon-coated copper grids, EMS

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 115000 X / Calibrated magnification: 115000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 210 nm / Calibrated defocus min: 210 nm / Calibrated defocus max: 3000 nm / Cs: 2 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: SIDE ENTRY, EUCENTRIC
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 466
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1DigitalMicrograph1.6image acquisition
3EMAN22.06CTF correction
6UCSF Chimera1.1model fitting
8Situs2.3model refinement
9NAMD2.1model refinement
10Coot0.8.1model refinement
14EMAN22.063D reconstruction
Image processingDetails: 432 symmetry
CTF correctionDetails: The ctf.auto function from EMAN2 was applied. / Type: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 4124
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 14.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4124 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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