[English] 日本語
![](img/lk-miru.gif)
- EMDB-8341: Architecture of the Yeast Mitochondrial Iron-Sulfur Cluster Assem... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-8341 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Architecture of the Yeast Mitochondrial Iron-Sulfur Cluster Assembly Machinery: the Sub-Complex Formed by the Iron Donor, Yfh1, and the Scaffold, Isu1 | |||||||||
![]() | Yfh1_Isu1 sub-complex | |||||||||
![]() |
| |||||||||
Function / homology | ![]() Mitochondrial iron-sulfur cluster biogenesis / Mitochondrial protein import / mitochondrial electron transport, succinate to ubiquinone / tRNA wobble uridine modification / iron chaperone activity / iron-sulfur cluster assembly complex / response to iron(II) ion / iron-sulfur cluster assembly / heme biosynthetic process / ferroxidase ...Mitochondrial iron-sulfur cluster biogenesis / Mitochondrial protein import / mitochondrial electron transport, succinate to ubiquinone / tRNA wobble uridine modification / iron chaperone activity / 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 | ![]() ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 17.5 Å | |||||||||
![]() | Ranatunga W / Gakh O / Galeano BK / Smith IV DY / Soderberg CA / Al-Karadaghi S / Thompson JR / Isaya G | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Architecture of the Yeast Mitochondrial Iron-Sulfur Cluster Assembly Machinery: THE SUB-COMPLEX FORMED BY THE IRON DONOR, Yfh1 PROTEIN, AND THE SCAFFOLD, Isu1 PROTEIN. Authors: Wasantha Ranatunga / Oleksandr Gakh / Belinda K Galeano / Douglas Y Smith / Christopher A G Söderberg / Salam Al-Karadaghi / James R Thompson / Grazia Isaya / ![]() ![]() Abstract: The biosynthesis of Fe-S clusters is a vital process involving the delivery of elemental iron and sulfur to scaffold proteins via molecular interactions that are still poorly defined. We ...The biosynthesis of Fe-S clusters is a vital process involving the delivery of elemental iron and sulfur to scaffold proteins via molecular interactions that are still poorly defined. We reconstituted a stable, functional complex consisting of the iron donor, Yfh1 (yeast frataxin homologue 1), and the Fe-S cluster scaffold, Isu1, with 1:1 stoichiometry, [Yfh1]24·[Isu1]24 Using negative staining transmission EM and single particle analysis, we obtained a three-dimensional reconstruction of this complex at a resolution of ∼17 Å. In addition, via chemical cross-linking, limited proteolysis, and mass spectrometry, we identified protein-protein interaction surfaces within the complex. The data together reveal that [Yfh1]24·[Isu1]24 is a roughly cubic macromolecule consisting of one symmetric Isu1 trimer binding on top of one symmetric Yfh1 trimer at each of its eight vertices. Furthermore, molecular modeling suggests that two subunits of the cysteine desulfurase, Nfs1, may bind symmetrically on top of two adjacent Isu1 trimers in a manner that creates two putative [2Fe-2S] cluster assembly centers. In each center, conserved amino acids known to be involved in sulfur and iron donation by Nfs1 and Yfh1, respectively, are in close proximity to the Fe-S cluster-coordinating residues of Isu1. We suggest that this architecture is suitable to ensure concerted and protected transfer of potentially toxic iron and sulfur atoms to Isu1 during Fe-S cluster assembly. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 11 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 15.7 KB 15.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12 KB | Display | ![]() |
Images | ![]() | 67.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 353 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 352.6 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 16 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5t0vMC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Yfh1_Isu1 sub-complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.034 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : Yfh1-Isu1
Entire | Name: Yfh1-Isu1 |
---|---|
Components |
|
-Supramolecule #1: Yfh1-Isu1
Supramolecule | Name: Yfh1-Isu1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: macromolecule comprising 24-mer of Yfh1 and 24-mer of Isu1 |
---|---|
Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
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 |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 15.383872 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 13.455976 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: VESSTDGQVV PQEVLNLPLE KAHEEADDYL DHLLDSLEEL SEAHPDCIPD VELSHGVMTL EIPAFGTYVI NKQPPNKQIW LASPLSGPN RFDLLNGEWV SLRNGTKLTD ILTEEVEKAI SK |
-Experimental details
-Structure determination
Method | negative staining |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 0.12 mg/mL | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.3 Component:
| |||||||||
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 |
---|---|
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: 559 / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
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 |
---|---|
Output model | ![]() PDB-5t0v: |