+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19145 | |||||||||
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Title | Closed Complex I from murine brain | |||||||||
Map data | composite map | |||||||||
Sample |
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Keywords | respiratory chain complex / mammalian mitochondria / MEMBRANE PROTEIN / ELECTRON TRANSPORT | |||||||||
Function / homology | Function and homology information 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 / RHOG GTPase cycle / Respiratory electron transport / protein insertion into mitochondrial inner membrane / circulatory system development ...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 / RHOG GTPase cycle / Respiratory electron transport / protein insertion into mitochondrial inner membrane / circulatory system development / blastocyst hatching / respiratory system process / psychomotor behavior / Mitochondrial protein degradation / response to light intensity / cellular response to oxygen levels / iron-sulfur cluster assembly complex / ubiquinone-6 biosynthetic process / mitochondrial large ribosomal subunit binding / gliogenesis / neural precursor cell proliferation / cardiac muscle tissue development / : / negative regulation of non-canonical NF-kappaB signal transduction / [2Fe-2S] cluster assembly / adult walking behavior / oxygen sensor activity / cellular response to glucocorticoid stimulus / response to hydroperoxide / positive regulation of mitochondrial membrane potential / cellular respiration / respiratory chain complex I / iron-sulfur cluster assembly / mitochondrial ribosome / adult behavior / mitochondrial translation / positive regulation of ATP biosynthetic process / 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 / cellular response to interferon-beta / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / neuron development / quinone binding / ATP synthesis coupled electron transport / 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 / visual perception / aerobic respiration / ionotropic glutamate receptor binding / response to hormone / Neutrophil degranulation / respiratory electron transport chain / reactive oxygen species metabolic process / neurogenesis / cerebellum development / regulation of mitochondrial membrane potential / kidney development / mitochondrion organization / response to cocaine / fatty acid metabolic process / cognition / synaptic membrane / mitochondrial membrane / apoptotic signaling pathway / sensory perception of sound / electron transport chain / response to nicotine / regulation of protein phosphorylation / response to hydrogen peroxide / multicellular organism growth / brain development / response to organic cyclic compound / negative regulation of cell growth / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / circadian rhythm / positive regulation of protein catabolic process / NAD binding / FMN binding / myelin sheath / nervous system development / 4 iron, 4 sulfur cluster binding Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 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. Cristallogr. / 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_19145.map.gz | 6.7 MB | EMDB map data format | |
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Header (meta data) | emd-19145-v30.xml emd-19145.xml | 67.2 KB 67.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19145_fsc.xml | 21.1 KB | Display | FSC data file |
Images | emd_19145.png | 100.4 KB | ||
Filedesc metadata | emd-19145.cif.gz | 14.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19145 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19145 | HTTPS FTP |
-Validation report
Summary document | emd_19145_validation.pdf.gz | 532 KB | Display | EMDB validaton report |
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Full document | emd_19145_full_validation.pdf.gz | 531.5 KB | Display | |
Data in XML | emd_19145_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | emd_19145_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19145 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19145 | HTTPS FTP |
-Related structure data
Related structure data | 8rgpMC 8pw5C 8pw6C 8pw7C 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_19145.map.gz / Format: CCP4 / Size: 31.7 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
-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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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 / 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 |
-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: FIELD EMISSION GUN |
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 |