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Yorodumi- EMDB-8458: Zinc and the Iron Donor Frataxin Regulate Oligomerization of the ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8458 | |||||||||
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Title | Zinc and the Iron Donor Frataxin Regulate Oligomerization of the Scaffold Protein to Form New Fe-S Cluster Assembly Centers | |||||||||
Map data | Iron sulfur cluster assembly protein 1 / Frataxin complex (generated using EMAN2) | |||||||||
Sample |
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Function / homology | Function and homology information Maturation of TCA enzymes and regulation of TCA cycle / Mitochondrial iron-sulfur cluster biogenesis / Mitochondrial protein import / mitochondrial electron transport, succinate to ubiquinone / iron chaperone activity / tRNA wobble uridine modification / iron-sulfur cluster assembly complex / response to iron(II) ion / iron-sulfur cluster assembly / heme biosynthetic process ...Maturation of TCA enzymes and regulation of TCA cycle / Mitochondrial iron-sulfur cluster biogenesis / Mitochondrial protein import / mitochondrial electron transport, succinate to ubiquinone / iron chaperone activity / tRNA wobble uridine modification / iron-sulfur cluster assembly complex / response to iron(II) ion / iron-sulfur cluster assembly / heme biosynthetic process / ferroxidase / ATPase activator activity / ferroxidase activity / glutathione metabolic process / ferric iron binding / ferrous iron binding / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / iron ion transport / intracellular iron ion homeostasis / response to oxidative stress / mitochondrial inner membrane / mitochondrial matrix / iron ion binding / mitochondrion / zinc ion binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 15.6 Å | |||||||||
Authors | Ranatunga W / Gakh O / Galeano BK / Smith IV DY / Thompson JR / Isaya G | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Metallomics / Year: 2017 Title: Zinc and the iron donor frataxin regulate oligomerization of the scaffold protein to form new Fe-S cluster assembly centers. Authors: B K Galeano / W Ranatunga / O Gakh / D Y Smith / J R Thompson / G Isaya / Abstract: Early studies of the bacterial Fe-S cluster assembly system provided structural details for how the scaffold protein and the cysteine desulfurase interact. This work and additional work on the yeast ...Early studies of the bacterial Fe-S cluster assembly system provided structural details for how the scaffold protein and the cysteine desulfurase interact. This work and additional work on the yeast and human systems elucidated a conserved mechanism for sulfur donation but did not provide any conclusive insights into the mechanism for iron delivery from the iron donor, frataxin, to the scaffold. We previously showed that oligomerization is a mechanism by which yeast frataxin (Yfh1) can promote assembly of the core machinery for Fe-S cluster synthesis both in vitro and in cells, in such a manner that the scaffold protein, Isu1, can bind to Yfh1 independent of the presence of the cysteine desulfurase, Nfs1. Here, in the absence of Yfh1, Isu1 was found to exist in two forms, one mostly monomeric with limited tendency to dimerize, and one with a strong propensity to oligomerize. Whereas the monomeric form is stabilized by zinc, the loss of zinc promotes formation of dimer and higher order oligomers. However, upon binding to oligomeric Yfh1, both forms take on a similar symmetrical trimeric configuration that places the Fe-S cluster coordinating residues of Isu1 in close proximity of iron-binding residues of Yfh1. This configuration is suitable for docking of Nfs1 in a manner that provides a structural context for coordinate iron and sulfur donation to the scaffold. Moreover, distinct structural features suggest that in physiological conditions the zinc-regulated abundance of monomeric vs. oligomeric Isu1 yields [Yfh1]·[Isu1] complexes with different Isu1 configurations that afford unique functional properties for Fe-S cluster assembly and delivery. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8458.map.gz | 19.2 MB | EMDB map data format | |
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Header (meta data) | emd-8458-v30.xml emd-8458.xml | 15 KB 15 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8458_fsc.xml | 12.1 KB | Display | FSC data file |
Images | emd_8458.png | 86.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8458 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8458 | HTTPS FTP |
-Validation report
Summary document | emd_8458_validation.pdf.gz | 376.9 KB | Display | EMDB validaton report |
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Full document | emd_8458_full_validation.pdf.gz | 376.4 KB | Display | |
Data in XML | emd_8458_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | emd_8458_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8458 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8458 | HTTPS FTP |
-Related structure data
Related structure data | 5treMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8458.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Iron sulfur cluster assembly protein 1 / Frataxin complex (generated using EMAN2) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.034 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Yfh1-Isu1
Entire | Name: Yfh1-Isu1 |
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Components |
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-Supramolecule #1: Yfh1-Isu1
Supramolecule | Name: Yfh1-Isu1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Macromolecular complex comprising 24-mer of Yfh1 and 24-mer of Isu1 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Recombinant expression | Organism: Escherichia coli #1/H766 (bacteria) / Recombinant plasmid: pET24a, pET28b |
Molecular weight | Theoretical: 700 KDa |
-Macromolecule #1: Iron sulfur cluster assembly protein 1, mitochondrial
Macromolecule | Name: Iron sulfur cluster assembly protein 1, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 15.383872 KDa |
Recombinant expression | Organism: Escherichia coli #1/H766 (bacteria) |
Sequence | String: GSHMSSITKR LYHPKVIEHY THPRNVGSLD KKLPNVGTGL VGAPACGDVM RLQIKVNDST GVIEDVKFKT FGCGSAIASS SYMTELVQG MTLDDAAKIK NTEIAKELSL PPVKLHCSML AEDAIKAAIK DYKSKRNTPT MLS |
-Macromolecule #2: Frataxin homolog, mitochondrial
Macromolecule | Name: Frataxin homolog, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 24 / Enantiomer: LEVO / EC number: ferroxidase |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 13.455976 KDa |
Recombinant expression | Organism: Escherichia coli #1/H766 (bacteria) |
Sequence | String: VESSTDGQVV PQEVLNLPLE KAHEEADDYL DHLLDSLEEL SEAHPDCIPD VELSHGVMTL EIPAFGTYVI NKQPPNKQIW LASPLSGPN RFDLLNGEWV SLRNGTKLTD ILTEEVEKAI SK |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.11 mg/mL | |||||||||
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Buffer | pH: 7.3 Component:
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Staining | Type: NEGATIVE / Material: uranyl acetate Details: Pre-incubated in HN100 buffer, the grid was placed on an 11 microliter drop of protein sample for 1 minute. Excess protein sample was blotted and washed for 3 seconds by placing the grid on ...Details: Pre-incubated in HN100 buffer, the grid was placed on an 11 microliter drop of protein sample for 1 minute. Excess protein sample was blotted and washed for 3 seconds by placing the grid on a drop of sterile water. After excess water was blotted, the grid was stained with 1% w/v uranyl acetate for 1 second and 30 seconds by successively placing it on two separate drops of uranyl acetate, with excess stain drawn off after each step. | |||||||||
Grid | Model: carbon-coated, EMS / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Details: DV-502A instrument, Denton Vacuum Inc. | |||||||||
Details | The protein complex was prepared by incubating Yfh1 and Isu1 (1:1.5 molar ratio) in HN100 buffer (10 mM HEPES-KOH, pH 7.3, 100 mM NaCl) and purified using Sephacryl S300 gel filtration chromatography. |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 475 / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 2.8 µm / Calibrated defocus min: 0.21 µm / Calibrated magnification: 115000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.8 µm / Nominal defocus min: 0.21 µm / Nominal magnification: 115000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-5tre: |