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Yorodumi- EMDB-10847: CIII2/CIV respiratory supercomplex from Saccharomyces cerevisiae -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10847 | |||||||||||||||
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Title | CIII2/CIV respiratory supercomplex from Saccharomyces cerevisiae | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Function / homology | Function and homology information matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial cytochrome c oxidase assembly / mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respirasome assembly / Mitochondrial protein degradation / : / : / cytochrome-c oxidase ...matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial cytochrome c oxidase assembly / mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respirasome assembly / Mitochondrial protein degradation / : / : / cytochrome-c oxidase / : / quinol-cytochrome-c reductase / cellular respiration / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / electron transport coupled proton transport / enzyme regulator activity / ATP synthesis coupled electron transport / proton transmembrane transport / nuclear periphery / mitochondrial membrane / aerobic respiration / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / mitochondrial inner membrane / copper ion binding / heme binding / mitochondrion / proteolysis / zinc ion binding / membrane / metal ion binding / cytosol Similarity search - Function | |||||||||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.17 Å | |||||||||||||||
Authors | Berndtsson J / Rathore S / Ott M | |||||||||||||||
Funding support | Sweden, 4 items
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Citation | Journal: EMBO Rep / Year: 2020 Title: Respiratory supercomplexes enhance electron transport by decreasing cytochrome c diffusion distance. Authors: Jens Berndtsson / Andreas Kohler / Sorbhi Rathore / Lorena Marin-Buera / Hannah Dawitz / Jutta Diessl / Verena Kohler / Antoni Barrientos / Sabrina Büttner / Flavia Fontanesi / Martin Ott / Abstract: Respiratory chains are crucial for cellular energy conversion and consist of multi-subunit complexes that can assemble into supercomplexes. These structures have been intensively characterized in ...Respiratory chains are crucial for cellular energy conversion and consist of multi-subunit complexes that can assemble into supercomplexes. These structures have been intensively characterized in various organisms, but their physiological roles remain unclear. Here, we elucidate their function by leveraging a high-resolution structural model of yeast respiratory supercomplexes that allowed us to inhibit supercomplex formation by mutation of key residues in the interaction interface. Analyses of a mutant defective in supercomplex formation, which still contains fully functional individual complexes, show that the lack of supercomplex assembly delays the diffusion of cytochrome c between the separated complexes, thus reducing electron transfer efficiency. Consequently, competitive cellular fitness is severely reduced in the absence of supercomplex formation and can be restored by overexpression of cytochrome c. In sum, our results establish how respiratory supercomplexes increase the efficiency of cellular energy conversion, thereby providing an evolutionary advantage for aerobic organisms. | |||||||||||||||
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_10847.map.gz | 171.1 MB | EMDB map data format | |
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Header (meta data) | emd-10847-v30.xml emd-10847.xml | 48.3 KB 48.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10847_fsc.xml | 14.5 KB | Display | FSC data file |
Images | emd_10847.png | 75.9 KB | ||
Masks | emd_10847_msk_1.map | 193.2 MB | Mask map | |
Others | emd_10847_half_map_1.map.gz emd_10847_half_map_2.map.gz | 170.4 MB 170.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10847 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10847 | HTTPS FTP |
-Validation report
Summary document | emd_10847_validation.pdf.gz | 422.7 KB | Display | EMDB validaton report |
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Full document | emd_10847_full_validation.pdf.gz | 421.8 KB | Display | |
Data in XML | emd_10847_validation.xml.gz | 19.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10847 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10847 | HTTPS FTP |
-Related structure data
Related structure data | 6ymxMC 6ymyC 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_10847.map.gz / Format: CCP4 / Size: 193.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10847_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Second half map
File | emd_10847_half_map_1.map | ||||||||||||
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Annotation | Second half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: First half map
File | emd_10847_half_map_2.map | ||||||||||||
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Annotation | First half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Respiratroy supercopmlex CIII2/CIV
+Supramolecule #1: Respiratroy supercopmlex CIII2/CIV
+Macromolecule #1: Cytochrome c oxidase subunit 1
+Macromolecule #2: Cytochrome c oxidase subunit 2
+Macromolecule #3: Cytochrome c oxidase subunit 3
+Macromolecule #4: Cytochrome c oxidase subunit 4, mitochondrial
+Macromolecule #5: Cytochrome c oxidase subunit 5A, mitochondrial
+Macromolecule #6: Cytochrome c oxidase subunit 6, mitochondrial
+Macromolecule #7: Cytochrome c oxidase subunit 7, mitochondrial
+Macromolecule #8: Cytochrome c oxidase subunit 8, mitochondrial
+Macromolecule #9: Cytochrome c oxidase subunit 9, mitochondrial
+Macromolecule #10: Cytochrome c oxidase subunit 12, mitochondrial
+Macromolecule #11: Cytochrome c oxidase subunit 13, mitochondrial
+Macromolecule #12: Cytochrome c oxidase subunit 26, mitochondrial
+Macromolecule #13: Cytochrome b-c1 complex subunit 1, mitochondrial
+Macromolecule #14: Cytochrome b-c1 complex subunit 2, mitochondrial
+Macromolecule #15: Cytochrome b
+Macromolecule #16: Cytochrome c1, heme protein, mitochondrial
+Macromolecule #17: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+Macromolecule #18: Cytochrome b-c1 complex subunit 6, mitochondrial
+Macromolecule #19: Cytochrome b-c1 complex subunit 7, mitochondrial
+Macromolecule #20: Cytochrome b-c1 complex subunit 8, mitochondrial
+Macromolecule #21: Cytochrome b-c1 complex subunit 9, mitochondrial
+Macromolecule #22: Cytochrome b-c1 complex subunit 6, mitochondrial
+Macromolecule #23: Cytochrome b-c1 complex subunit 9, mitochondrial
+Macromolecule #24: Cytochrome b-c1 complex subunit 10, mitochondrial
+Macromolecule #25: Cytochrome b-c1 complex subunit 10, mitochondrial
+Macromolecule #26: COPPER (II) ION
+Macromolecule #27: HEME-A
+Macromolecule #28: PHOSPHATIDYLETHANOLAMINE
+Macromolecule #29: (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16...
+Macromolecule #30: DINUCLEAR COPPER ION
+Macromolecule #31: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
+Macromolecule #32: ZINC ION
+Macromolecule #33: (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate
+Macromolecule #34: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #35: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradeca...
+Macromolecule #36: (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-penta...
+Macromolecule #37: 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)...
+Macromolecule #38: (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoy...
+Macromolecule #39: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
+Macromolecule #40: FE2/S2 (INORGANIC) CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Component:
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Grid | Model: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number real images: 8775 / Average exposure time: 9.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -0.003 µm / Nominal defocus min: -0.0014 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |