+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17991 | |||||||||
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Title | A respirasome from murine liver | |||||||||
Map data | composite map, used to build the model | |||||||||
Sample |
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Keywords | Respiratory chain super complex / mammalian mitochondria / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information Complex IV assembly / Complex III assembly / subthalamus development / pons development / TP53 Regulates Metabolic Genes / response to injury involved in regulation of muscle adaptation / Protein lipoylation / reproductive system development / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis ...Complex IV assembly / Complex III assembly / subthalamus development / pons development / TP53 Regulates Metabolic Genes / response to injury involved in regulation of muscle adaptation / Protein lipoylation / reproductive system development / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / Mitochondrial protein import / cerebellar Purkinje cell layer development / RHOG GTPase cycle / respiratory chain complex III / Respiratory electron transport / protein insertion into mitochondrial inner membrane / circulatory system development / blastocyst hatching / respiratory chain complex IV assembly / pyramidal neuron development / response to mercury ion / mitochondrial respirasome assembly / Cytoprotection by HMOX1 / mitochondrial respiratory chain complex III assembly / thalamus development / respiratory system process / respiratory chain complex IV / psychomotor behavior / Mitochondrial protein degradation / regulation of oxidative phosphorylation / response to light intensity / cellular response to oxygen levels / iron-sulfur cluster assembly complex / ubiquinone-6 biosynthetic process / mitochondrial large ribosomal subunit binding / : / gliogenesis / : / response to alkaloid / neural precursor cell proliferation / oxidative phosphorylation / cytochrome-c oxidase / cardiac muscle tissue development / : / negative regulation of non-canonical NF-kappaB signal transduction / [2Fe-2S] cluster assembly / quinol-cytochrome-c reductase / adult walking behavior / oxygen sensor activity / response to copper ion / response to glucagon / cellular response to glucocorticoid stimulus / ubiquinol-cytochrome-c reductase activity / response to hydroperoxide / positive regulation of mitochondrial membrane potential / mitochondrial electron transport, cytochrome c to oxygen / cellular respiration / cytochrome-c oxidase activity / respiratory chain complex I / iron-sulfur cluster assembly / mitochondrial ribosome / midbrain development / hypothalamus development / mitochondrial electron transport, ubiquinol to cytochrome c / adult behavior / mitochondrial translation / positive regulation of ATP biosynthetic process / response to cobalamin / dopamine metabolic process / positive regulation of execution phase of apoptosis / NADH:ubiquinone reductase (H+-translocating) / : / ubiquinone binding / NADH dehydrogenase activity / apoptotic mitochondrial changes / : / mitochondrial ATP synthesis coupled electron transport / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / proton motive force-driven mitochondrial ATP synthesis / electron transport coupled proton transport / acyl binding / response to hyperoxia / cellular response to interferon-beta / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / neuron development / animal organ regeneration / quinone binding / response to cadmium ion / enzyme regulator activity / ATP synthesis coupled electron transport / response to electrical stimulus / cellular response to retinoic acid / negative regulation of intrinsic apoptotic signaling pathway / muscle contraction / negative regulation of reactive oxygen species biosynthetic process / ATP metabolic process / extrinsic apoptotic signaling pathway / tricarboxylic acid cycle Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Vercellino I / Sazanov LA | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: 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: 2018 Title: Real-space refinement in PHENIX for cryo-EM and crystallography Authors: Afonine PV / Adams PD | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17991.map.gz | 11.3 MB | EMDB map data format | |
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Header (meta data) | emd-17991-v30.xml emd-17991.xml | 92.9 KB 92.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17991_fsc.xml | 21.2 KB | Display | FSC data file |
Images | emd_17991.png | 42.5 KB | ||
Filedesc metadata | emd-17991.cif.gz | 18.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17991 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17991 | HTTPS FTP |
-Validation report
Summary document | emd_17991_validation.pdf.gz | 563 KB | Display | EMDB validaton report |
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Full document | emd_17991_full_validation.pdf.gz | 562.6 KB | Display | |
Data in XML | emd_17991_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | emd_17991_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17991 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17991 | HTTPS FTP |
-Related structure data
Related structure data | 8pw7MC 8pw5C 8pw6C 8rgpC 8rgqC 8rgrC 8rgtC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17991.map.gz / Format: CCP4 / Size: 50.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | composite map, used to build the model | ||||||||||||||||||||||||||||||||||||
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
-Sample components
+Entire : A respirasome from murine liver
+Supramolecule #1: A respirasome from murine liver
+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 isoform 1, mitochondrial
+Macromolecule #5: Cytochrome c oxidase subunit 5A, mitochondrial
+Macromolecule #6: Cytochrome c oxidase subunit 5B, mitochondrial
+Macromolecule #7: Cytochrome c oxidase subunit 6A1, mitochondrial
+Macromolecule #8: Cytochrome c oxidase subunit 6B1
+Macromolecule #9: Cytochrome c oxidase subunit 6C
+Macromolecule #10: Cytochrome c oxidase subunit 7B, mitochondrial
+Macromolecule #11: Cytochrome c oxidase subunit 7C, mitochondrial
+Macromolecule #12: Cytochrome c oxidase subunit 7A2, 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 7
+Macromolecule #19: Cytochrome b-c1 complex subunit 8
+Macromolecule #20: Cytochrome b-c1 complex subunit 6, mitochondrial
+Macromolecule #21: Cytochrome b-c1 complex subunit 9
+Macromolecule #22: Cytochrome b-c1 complex subunit 10
+Macromolecule #23: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+Macromolecule #24: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+Macromolecule #25: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+Macromolecule #26: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+Macromolecule #27: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #28: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+Macromolecule #29: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+Macromolecule #30: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+Macromolecule #31: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #32: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #33: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #34: Acyl carrier protein, mitochondrial
+Macromolecule #35: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+Macromolecule #36: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #37: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+Macromolecule #39: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+Macromolecule #40: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #41: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #42: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #43: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #44: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #45: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #46: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #47: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #48: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #49: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+Macromolecule #50: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #51: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #52: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+Macromolecule #53: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+Macromolecule #54: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #55: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #56: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+Macromolecule #57: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+Macromolecule #58: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+Macromolecule #59: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+Macromolecule #60: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+Macromolecule #61: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+Macromolecule #62: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #63: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+Macromolecule #64: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #65: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #66: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+Macromolecule #67: Cytochrome c oxidase subunit 8A, mitochondrial
+Macromolecule #68: COPPER (II) ION
+Macromolecule #69: SODIUM ION
+Macromolecule #70: HEME-A
+Macromolecule #71: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #72: MAGNESIUM ION
+Macromolecule #73: DINUCLEAR COPPER ION
+Macromolecule #74: ZINC ION
+Macromolecule #75: TRISTEAROYLGLYCEROL
+Macromolecule #76: CARDIOLIPIN
+Macromolecule #77: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #78: HEME C
+Macromolecule #79: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #80: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+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 |
-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 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 1 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec. | ||||||||||||
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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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 |