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Open data
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Basic information
| Entry | ![]() | |||||||||
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| Title | C respirasome from murine liver | |||||||||
Map data | composite map | |||||||||
Sample |
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Keywords | Respiratory chain super complex / mammalian mitochondria / MEMBRANE PROTEIN | |||||||||
| Function / homology | Function and homology informationComplex IV assembly / response to D-galactosamine / Complex III assembly / TP53 Regulates Metabolic Genes / Mitochondrial protein import / response to injury involved in regulation of muscle adaptation / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / RHOG GTPase cycle ...Complex IV assembly / response to D-galactosamine / Complex III assembly / TP53 Regulates Metabolic Genes / Mitochondrial protein import / response to injury involved in regulation of muscle adaptation / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / RHOG GTPase cycle / respiratory chain complex IV assembly / response to mercury ion / Cytoprotection by HMOX1 / subthalamus development / pons development / Respiratory electron transport / protein insertion into mitochondrial inner membrane / response to cobalamin / cerebellar Purkinje cell layer development / aerobic electron transport chain / mitochondrial respiratory chain complex III assembly / blastocyst hatching / respiratory system process / pyramidal neuron development / respiratory chain complex IV / psychomotor behavior / response to alkaloid / cellular respiration / thalamus development / Mitochondrial protein degradation / cellular response to oxygen levels / response to light intensity / mesenchymal stem cell proliferation / reproductive system development / iron-sulfur cluster assembly complex / respiratory chain complex / mitochondrial [2Fe-2S] assembly complex / mitochondrial large ribosomal subunit binding / gliogenesis / cytochrome-c oxidase / mesenchymal stem cell differentiation / circulatory system development / respiratory chain complex III / oxidative phosphorylation / negative regulation of non-canonical NF-kappaB signal transduction / quinol-cytochrome-c reductase / cardiac muscle tissue development / mitochondrial electron transport, cytochrome c to oxygen / neural precursor cell proliferation / [2Fe-2S] cluster assembly / adult walking behavior / response to glucagon / oxygen sensor activity / positive regulation of mitochondrial membrane potential / response to hydroperoxide / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / cellular response to glucocorticoid stimulus / stem cell division / response to copper ion / mitochondrial electron transport, ubiquinol to cytochrome c / NADH dehydrogenase activity / iron-sulfur cluster assembly / hypothalamus development / midbrain development / electron transport coupled proton transport / dopamine metabolic process / NADH:ubiquinone reductase (H+-translocating) / adult behavior / mitochondrial ATP synthesis coupled electron transport / positive regulation of ATP biosynthetic process / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / response to electrical stimulus / respiratory chain complex I / animal organ regeneration / response to hyperoxia / positive regulation of execution phase of apoptosis / NADH dehydrogenase (ubiquinone) activity / response to cadmium ion / neuron development / quinone binding / cellular response to interferon-beta / ATP synthesis coupled electron transport / response to hormone / negative regulation of reactive oxygen species biosynthetic process / extrinsic apoptotic signaling pathway / tricarboxylic acid cycle / cellular response to retinoic acid / lactation / neurogenesis / Neutrophil degranulation / visual perception / response to nutrient / muscle contraction / reactive oxygen species metabolic process / aerobic respiration / cerebellum development / central nervous system development Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Vercellino I / Sazanov LA | |||||||||
| Funding support | European Union, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024Title: SCAF1 drives the compositional diversity of mammalian respirasomes. Authors: Irene Vercellino / Leonid A Sazanov / ![]() Abstract: Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies ...Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies have shown that different tissues/organs are equipped with specific sets of supercomplexes, depending on their metabolic needs, the notion that supercomplexes have a role in the regulation of metabolism has been challenged. However, irrespective of the mechanistic conclusions, the composition of various high molecular weight supercomplexes remains uncertain. Here, using cryogenic electron microscopy, we demonstrate that mammalian (mouse) tissues contain three defined types of 'respirasome', supercomplexes made of CI, CIII and CIV. The stoichiometry and position of CIV differs in the three respirasomes, of which only one contains the supercomplex-associated factor SCAF1, whose involvement in respirasome formation has long been contended. Our structures confirm that the 'canonical' respirasome (the C-respirasome, CICIIICIV) does not contain SCAF1, which is instead associated to a different respirasome (the CS-respirasome), containing a second copy of CIV. We also identify an alternative respirasome (A-respirasome), with CIV bound to the 'back' of CI, instead of the 'toe'. This structural characterization of mouse mitochondrial supercomplexes allows us to hypothesize a mechanistic basis for their specific role in different metabolic conditions. #1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018Title: Real-space refinement in PHENIX for cryo-EM and crystallography Authors: Afonine PV / Adams PD | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_17990.map.gz | 8.7 MB | EMDB map data format | |
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| Header (meta data) | emd-17990-v30.xml emd-17990.xml | 95.2 KB 95.2 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_17990_fsc.xml | 21.2 KB | Display | FSC data file |
| Images | emd_17990.png | 76.9 KB | ||
| Filedesc metadata | emd-17990.cif.gz | 18.8 KB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17990 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17990 | HTTPS FTP |
-Validation report
| Summary document | emd_17990_validation.pdf.gz | 562.1 KB | Display | EMDB validaton report |
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| Full document | emd_17990_full_validation.pdf.gz | 561.7 KB | Display | |
| Data in XML | emd_17990_validation.xml.gz | 13.3 KB | Display | |
| Data in CIF | emd_17990_validation.cif.gz | 19.8 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17990 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17990 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8pw6MC ![]() 8pw5C ![]() 8pw7C ![]() 8rgpC ![]() 8rgqC ![]() 8rgrC ![]() 8rgtC C: citing same article ( M: atomic model generated by this map |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_17990.map.gz / Format: CCP4 / Size: 54.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | composite map | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : C respirasome from murine liver
+Supramolecule #1: C respirasome from murine liver
+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 c oxidase subunit 1
+Macromolecule #12: Cytochrome c oxidase subunit 2
+Macromolecule #13: Cytochrome c oxidase subunit 3
+Macromolecule #14: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
+Macromolecule #15: Cytochrome c oxidase subunit 5A, mitochondrial
+Macromolecule #16: Cytochrome c oxidase subunit 5B, mitochondrial
+Macromolecule #17: Cytochrome c oxidase subunit 6A1, mitochondrial
+Macromolecule #18: Cytochrome c oxidase subunit 6B1
+Macromolecule #19: Cytochrome c oxidase subunit 6C
+Macromolecule #20: Cytochrome c oxidase subunit 7B, mitochondrial
+Macromolecule #21: Cytochrome c oxidase subunit 7C, mitochondrial
+Macromolecule #22: Cytochrome c oxidase subunit 8A, mitochondrial
+Macromolecule #23: Cytochrome c oxidase subunit 7A2, mitochondrial
+Macromolecule #24: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+Macromolecule #25: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+Macromolecule #26: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+Macromolecule #27: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+Macromolecule #28: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #29: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+Macromolecule #30: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+Macromolecule #31: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+Macromolecule #32: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #33: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #34: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #35: Acyl carrier protein, mitochondrial
+Macromolecule #36: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+Macromolecule #37: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #39: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+Macromolecule #40: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+Macromolecule #41: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #42: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #43: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #44: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #45: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #46: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #47: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #48: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #49: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #50: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+Macromolecule #51: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #52: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #53: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+Macromolecule #54: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+Macromolecule #55: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #56: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #57: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+Macromolecule #58: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+Macromolecule #59: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+Macromolecule #60: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+Macromolecule #61: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+Macromolecule #62: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+Macromolecule #63: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #64: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+Macromolecule #65: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #66: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #67: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+Macromolecule #68: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #69: CARDIOLIPIN
+Macromolecule #70: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #71: HEME C
+Macromolecule #72: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #73: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #74: COPPER (II) ION
+Macromolecule #75: SODIUM ION
+Macromolecule #76: HEME-A
+Macromolecule #77: MAGNESIUM ION
+Macromolecule #78: DINUCLEAR COPPER ION
+Macromolecule #79: ZINC ION
+Macromolecule #80: TRISTEAROYLGLYCEROL
+Macromolecule #81: IRON/SULFUR CLUSTER
+Macromolecule #82: FLAVIN MONONUCLEOTIDE
+Macromolecule #83: POTASSIUM ION
+Macromolecule #84: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #85: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #86: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Concentration | 0.3 mg/mL | ||||||||||||
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| Buffer | pH: 7.7 Component:
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| Grid | Model: Quantifoil R0.6/1 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 1 | ||||||||||||
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
| Microscope | FEI TITAN KRIOS |
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| Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 9453 / Average exposure time: 4.4 sec. / Average electron dose: 80.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000 |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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FIELD EMISSION GUN



