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Open data
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Basic information
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Title | Closed Complex I from murine brain | |||||||||
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![]() | respiratory chain complex / mammalian mitochondria / MEMBRANE PROTEIN / ELECTRON TRANSPORT | |||||||||
Function / homology | ![]() Mitochondrial protein import / response to injury involved in regulation of muscle adaptation / mesenchymal stem cell proliferation / reproductive system development / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / RHOG GTPase cycle / Respiratory electron transport / protein insertion into mitochondrial inner membrane ...Mitochondrial protein import / response to injury involved in regulation of muscle adaptation / mesenchymal stem cell proliferation / reproductive system development / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / Complex I biogenesis / RHOG GTPase cycle / Respiratory electron transport / protein insertion into mitochondrial inner membrane / mesenchymal stem cell differentiation / circulatory system development / blastocyst hatching / respiratory system process / psychomotor behavior / Mitochondrial protein degradation / cellular response to oxygen levels / stem cell division / respiratory chain complex / response to light intensity / mitochondrial [2Fe-2S] assembly complex / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding / gliogenesis / negative regulation of non-canonical NF-kappaB signal transduction / cardiac muscle tissue development / neural precursor cell proliferation / positive regulation of mitochondrial membrane potential / [2Fe-2S] cluster assembly / adult walking behavior / cellular response to glucocorticoid stimulus / oxygen sensor activity / response to hydroperoxide / iron-sulfur cluster assembly / positive regulation of ATP biosynthetic process / dopamine metabolic process / adult behavior / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I assembly / positive regulation of execution phase of apoptosis / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase activity / proton motive force-driven mitochondrial ATP synthesis / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / neuron development / quinone binding / cellular response to interferon-beta / ATP synthesis coupled electron transport / cellular response to retinoic acid / negative regulation of reactive oxygen species biosynthetic process / extrinsic apoptotic signaling pathway / neurogenesis / tricarboxylic acid cycle / muscle contraction / Neutrophil degranulation / visual perception / cerebellum development / reactive oxygen species metabolic process / DNA damage response, signal transduction by p53 class mediator / aerobic respiration / regulation of mitochondrial membrane potential / respiratory electron transport chain / kidney development / fatty acid metabolic process / mitochondrion organization / response to nicotine / sensory perception of sound / response to cocaine / monooxygenase activity / electron transport chain / mitochondrial membrane / brain development / : / multicellular organism growth / response to hydrogen peroxide / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / cognition / circadian rhythm / positive regulation of protein catabolic process / NAD binding / fatty acid biosynthetic process / cellular senescence / FMN binding / nervous system development / myelin sheath / 4 iron, 4 sulfur cluster binding / neuron apoptotic process / gene expression / response to oxidative stress / in utero embryonic development / response to ethanol / electron transfer activity / response to hypoxia / mitochondrial inner membrane / nuclear speck / nuclear body / mitochondrial matrix / inflammatory response Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
![]() | Vercellino I / Sazanov LA | |||||||||
Funding support | European Union, 1 items
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![]() | ![]() 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: ![]() Title: Real-space refinement in PHENIX for cryo-EM and crystallography Authors: Afonine PV / Adams PD | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 6.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 67.2 KB 67.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 21.1 KB | Display | ![]() |
Images | ![]() | 100.4 KB | ||
Filedesc metadata | ![]() | 14.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8rgpMC ![]() 8pw5C ![]() 8pw6C ![]() 8pw7C ![]() 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 ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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 : Closed Complex I from murine brain
+Supramolecule #1: Closed Complex I from murine brain
+Macromolecule #1: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+Macromolecule #2: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+Macromolecule #3: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+Macromolecule #4: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+Macromolecule #5: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #6: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+Macromolecule #7: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+Macromolecule #8: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+Macromolecule #9: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #10: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #11: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #12: Acyl carrier protein, mitochondrial
+Macromolecule #13: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+Macromolecule #14: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #15: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #16: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+Macromolecule #17: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+Macromolecule #18: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #19: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #20: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #21: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #22: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #23: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #24: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #25: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #26: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+Macromolecule #28: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #29: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #30: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+Macromolecule #31: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+Macromolecule #32: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #33: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #34: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+Macromolecule #35: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+Macromolecule #36: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+Macromolecule #37: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+Macromolecule #39: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+Macromolecule #40: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #41: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+Macromolecule #42: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #43: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #44: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+Macromolecule #45: IRON/SULFUR CLUSTER
+Macromolecule #46: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #47: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #48: Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer
+Macromolecule #49: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #50: FLAVIN MONONUCLEOTIDE
+Macromolecule #51: POTASSIUM ION
+Macromolecule #52: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #53: ZINC ION
+Macromolecule #54: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #55: CARDIOLIPIN
+Macromolecule #56: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #57: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | 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: 10416 / Average exposure time: 4.4 sec. / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.6 µm / Calibrated defocus min: 0.6 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 |