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Yorodumi- EMDB-12702: Murine supercomplex CIII2CIV in the assembled locked conformation -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12702 | |||||||||
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Title | Murine supercomplex CIII2CIV in the assembled locked conformation | |||||||||
Map data | CIIICIV full, locked conformation | |||||||||
Sample |
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Function / homology | Function and homology information Complex IV assembly / Complex III assembly / subthalamus development / pons development / TP53 Regulates Metabolic Genes / cerebellar Purkinje cell layer development / respiratory chain complex III / Respiratory electron transport / respiratory chain complex IV assembly / pyramidal neuron development ...Complex IV assembly / Complex III assembly / subthalamus development / pons development / TP53 Regulates Metabolic Genes / cerebellar Purkinje cell layer development / respiratory chain complex III / Respiratory electron transport / respiratory chain complex IV assembly / pyramidal neuron development / response to mercury ion / Cytoprotection by HMOX1 / mitochondrial respiratory chain complex III assembly / thalamus development / respiratory chain complex IV / Mitochondrial protein degradation / : / : / response to alkaloid / oxidative phosphorylation / cytochrome-c oxidase / quinol-cytochrome-c reductase / response to copper ion / response to glucagon / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cellular respiration / cytochrome-c oxidase activity / midbrain development / hypothalamus development / mitochondrial electron transport, ubiquinol to cytochrome c / response to cobalamin / electron transport coupled proton transport / response to hyperoxia / animal organ regeneration / response to cadmium ion / enzyme regulator activity / ATP synthesis coupled electron transport / response to electrical stimulus / lactation / response to hormone / respiratory electron transport chain / cerebellum development / response to activity / central nervous system development / hippocampus development / mitochondrial membrane / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / response to toxic substance / response to calcium ion / myelin sheath / response to ethanol / response to oxidative stress / mitochondrial inner membrane / oxidoreductase activity / response to hypoxia / response to xenobiotic stimulus / copper ion binding / ubiquitin protein ligase binding / heme binding / protein-containing complex binding / protein-containing complex / mitochondrion / proteolysis / nucleoplasm / membrane / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) / Mouse (mice) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Vercellino I / Sazanov LA | |||||||||
Funding support | Austria, 1 items
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Citation | Journal: Nature / Year: 2021 Title: Structure and assembly of the mammalian mitochondrial supercomplex CIIICIV. Authors: Irene Vercellino / Leonid A Sazanov / Abstract: The enzymes of the mitochondrial electron transport chain are key players of cell metabolism. Despite being active when isolated, in vivo they associate into supercomplexes, whose precise role is ...The enzymes of the mitochondrial electron transport chain are key players of cell metabolism. Despite being active when isolated, in vivo they associate into supercomplexes, whose precise role is debated. Supercomplexes CIIICIV (refs. ), CICIII (ref. ) and CICIIICIV (respirasome) exist in mammals, but in contrast to CICIII and the respirasome, to date the only known eukaryotic structures of CIIICIV come from Saccharomyces cerevisiae and plants, which have different organization. Here we present the first, to our knowledge, structures of mammalian (mouse and ovine) CIIICIV and its assembly intermediates, in different conformations. We describe the assembly of CIIICIV from the CIII precursor to the final CIIICIV conformation, driven by the insertion of the N terminus of the assembly factor SCAF1 (ref. ) deep into CIII, while its C terminus is integrated into CIV. Our structures (which include CICIII and the respirasome) also confirm that SCAF1 is exclusively required for the assembly of CIIICIV and has no role in the assembly of the respirasome. We show that CIII is asymmetric due to the presence of only one copy of subunit 9, which straddles both monomers and prevents the attachment of a second copy of SCAF1 to CIII, explaining the presence of one copy of CIV in CIIICIV in mammals. Finally, we show that CIII and CIV gain catalytic advantage when assembled into the supercomplex and propose a role for CIIICIV in fine tuning the efficiency of electron transfer in the electron transport chain. | |||||||||
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_12702.map.gz | 4 MB | EMDB map data format | |
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Header (meta data) | emd-12702-v30.xml emd-12702.xml | 43.6 KB 43.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12702_fsc.xml | 18.6 KB | Display | FSC data file |
Images | emd_12702.png | 171.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12702 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12702 | HTTPS FTP |
-Validation report
Summary document | emd_12702_validation.pdf.gz | 362.2 KB | Display | EMDB validaton report |
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Full document | emd_12702_full_validation.pdf.gz | 361.7 KB | Display | |
Data in XML | emd_12702_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | emd_12702_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12702 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12702 | HTTPS FTP |
-Related structure data
Related structure data | 7o37MC 7o3cC 7o3eC 7o3hC 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_12702.map.gz / Format: CCP4 / Size: 20.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CIIICIV full, locked conformation | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.064 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 : Murine full supercomplex CIII2CIV in the locked conformation
+Supramolecule #1: Murine full supercomplex CIII2CIV in the locked conformation
+Macromolecule #1: Cytochrome b-c1 complex subunit 1, mitochondrial
+Macromolecule #2: Cytochrome b-c1 complex subunit 2, mitochondrial
+Macromolecule #3: Cytochrome b
+Macromolecule #4: Cytochrome c1, heme protein, mitochondrial
+Macromolecule #5: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+Macromolecule #6: Cytochrome b-c1 complex subunit 7
+Macromolecule #7: Cytochrome b-c1 complex subunit 8
+Macromolecule #8: Cytochrome b-c1 complex subunit 6, mitochondrial
+Macromolecule #9: Cytochrome b-c1 complex subunit 9
+Macromolecule #10: Cytochrome b-c1 complex subunit 10
+Macromolecule #11: Cytochrome b-c1 complex subunit 9
+Macromolecule #12: Cox7a2l protein
+Macromolecule #13: Cytochrome c oxidase subunit 1
+Macromolecule #14: Cytochrome c oxidase subunit 2
+Macromolecule #15: Cytochrome c oxidase subunit 3
+Macromolecule #16: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
+Macromolecule #17: Cytochrome c oxidase subunit 5A, mitochondrial
+Macromolecule #18: Cytochrome c oxidase subunit 5B, mitochondrial
+Macromolecule #19: Cytochrome c oxidase subunit 6A2, mitochondrial
+Macromolecule #20: Cytochrome c oxidase subunit 6B1
+Macromolecule #21: Cytochrome c oxidase subunit 6C
+Macromolecule #22: Cytochrome c oxidase subunit 7B, mitochondrial
+Macromolecule #23: Cytochrome c oxidase subunit 7C, mitochondrial
+Macromolecule #24: Cytochrome c oxidase subunit 8B, mitochondrial
+Macromolecule #25: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #26: CARDIOLIPIN
+Macromolecule #27: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #28: HEME C
+Macromolecule #29: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #30: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #31: TRISTEAROYLGLYCEROL
+Macromolecule #32: COPPER (II) ION
+Macromolecule #33: SODIUM ION
+Macromolecule #34: HEME-A
+Macromolecule #35: MAGNESIUM ION
+Macromolecule #36: DINUCLEAR COPPER ION
+Macromolecule #37: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4 mg/mL | |||||||||||||||
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Buffer | pH: 7.7 Component:
Details: CHAPS was added only upon freezing | |||||||||||||||
Grid | Model: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 1.0 nm / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 7245 / Average exposure time: 1.17 sec. / Average electron dose: 90.66 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.7 µm / Calibrated defocus min: 0.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |