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Yorodumi- EMDB-10334: Complex IV in the III2-IV2 mitochondrial respiratory supercomplex... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10334 | |||||||||
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Title | Complex IV in the III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae (CIV(5B)-b)Cytochrome c oxidase | |||||||||
Map data | Complex IV in the III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae (CIV(5B)-b)Cytochrome c oxidase | |||||||||
Sample |
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Biological species | Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Marechal A / Hartley A / Pinotsis N | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: Rcf2 revealed in cryo-EM structures of hypoxic isoforms of mature mitochondrial III-IV supercomplexes. Authors: Andrew M Hartley / Brigitte Meunier / Nikos Pinotsis / Amandine Maréchal / Abstract: The organization of the mitochondrial electron transport chain proteins into supercomplexes (SCs) is now undisputed; however, their assembly process, or the role of differential expression isoforms, ...The organization of the mitochondrial electron transport chain proteins into supercomplexes (SCs) is now undisputed; however, their assembly process, or the role of differential expression isoforms, remain to be determined. In , cytochrome oxidase (CIV) forms SCs of varying stoichiometry with cytochrome (CIII). Recent studies have revealed, in normoxic growth conditions, an interface made exclusively by Cox5A, the only yeast respiratory protein that exists as one of two isoforms depending on oxygen levels. Here we present the cryo-EM structures of the III-IV and III-IV SCs containing the hypoxic isoform Cox5B solved at 3.4 and 2.8 Å, respectively. We show that the change of isoform does not affect SC formation or activity, and that SC stoichiometry is dictated by the level of CIII/CIV biosynthesis. Comparison of the CIV- and CIV-containing SC structures highlighted few differences, found mainly in the region of Cox5. Additional density was revealed in all SCs, independent of the CIV isoform, in a pocket formed by Cox1, Cox3, Cox12, and Cox13, away from the CIII-CIV interface. In the CIV-containing hypoxic SCs, this could be confidently assigned to the hypoxia-induced gene 1 (Hig1) type 2 protein Rcf2. With conserved residues in mammalian Hig1 proteins and Cox3/Cox12/Cox13 orthologs, we propose that Hig1 type 2 proteins are stoichiometric subunits of CIV, at least when within a III-IV SC. | |||||||||
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_10334.map.gz | 303.5 MB | EMDB map data format | |
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Header (meta data) | emd-10334-v30.xml emd-10334.xml | 19.3 KB 19.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10334_fsc.xml | 15.6 KB | Display | FSC data file |
Images | emd_10334.png | 79.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10334 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10334 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10334.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Complex IV in the III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae (CIV(5B)-b) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.085 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 : Complex IV in the III2-IV2 mitochondrial respiratory supercomplex...
+Supramolecule #1: Complex IV in the III2-IV2 mitochondrial respiratory supercomplex...
+Macromolecule #1: Cox1 Cytochrome c oxidase subunit 1
+Macromolecule #2: Cox2Cytochrome c oxidase subunit 2
+Macromolecule #3: Cox3 Cytochrome c oxidase subunit 3
+Macromolecule #4: Cox4 Cytochrome c oxidase subunit 4
+Macromolecule #5: Cox5B Cytochrome c oxidase subunit 5B
+Macromolecule #6: Cox6 Cytochrome c oxidase subunit 6
+Macromolecule #7: Cox7 Cytochrome c oxidase subunit 7
+Macromolecule #8: Cox8 Cytochrome c oxidase subunit 8
+Macromolecule #9: Cox9 Cytochrome c oxidase subunit 7A
+Macromolecule #10: Cox12 Cytochrome c oxidase subunit 6B
+Macromolecule #11: Cox13 Cytochrome c oxidase subunit 6A
+Macromolecule #12: Cox26, Uncharacterized protein YDR119W-A
+Macromolecule #13: RCF2, Respiratory supercomplex factor 2, mitochondrial
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV Details: 3 microliter of sample applied to negatively glow discharged grid, blot force -10; blotting time 8.5 sec.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 56.4 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |