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Yorodumi- EMDB-1876: Structural basis of substrate shuttling in bovine mitochondrial s... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1876 | |||||||||
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Title | Structural basis of substrate shuttling in bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM | |||||||||
Map data | 3D cryo-EM map of supercomplex B (I1III2IV1) from bovine heart mitochondria | |||||||||
Sample |
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Keywords | Supercomplex B / mitochondria / respiratory chain / complex I / complex III / complex IV / amphipol A8-35 / random conical tilt | |||||||||
Function / homology | Function and homology information Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Pyroptosis / Regulation of the apoptosome activity / Transcriptional activation of mitochondrial biogenesis / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly ...Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Pyroptosis / Regulation of the apoptosome activity / Transcriptional activation of mitochondrial biogenesis / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / : / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / mitochondrial respirasome assembly / respiratory chain complex IV / : / regulation of oxidative phosphorylation / Respiratory electron transport / : / cytochrome-c oxidase / : / oxidative phosphorylation / quinol-cytochrome-c reductase / molybdopterin cofactor binding / respiratory chain complex I / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / iron-sulfur cluster assembly / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / NADH dehydrogenase activity / : / ubiquinone binding / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity / quinone binding / electron transport coupled proton transport / ATP synthesis coupled electron transport / enzyme regulator activity / aerobic respiration / respiratory electron transport chain / ferric iron binding / central nervous system development / mitochondrial membrane / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / electron transfer activity / iron ion binding / copper ion binding / apoptotic process / heme binding / mitochondrion / proteolysis / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 19.0 Å | |||||||||
Authors | Althoff T / Mills DJ / Popot J-L / Kuehlbrandt W | |||||||||
Citation | Journal: EMBO J / Year: 2011 Title: Arrangement of electron transport chain components in bovine mitochondrial supercomplex I1III2IV1. Authors: Thorsten Althoff / Deryck J Mills / Jean-Luc Popot / Werner Kühlbrandt / Abstract: The respiratory chain in the inner mitochondrial membrane contains three large multi-enzyme complexes that together establish the proton gradient for ATP synthesis, and assemble into a supercomplex. ...The respiratory chain in the inner mitochondrial membrane contains three large multi-enzyme complexes that together establish the proton gradient for ATP synthesis, and assemble into a supercomplex. A 19-Å 3D map of the 1.7-MDa amphipol-solubilized supercomplex I(1)III(2)IV(1) from bovine heart obtained by single-particle electron cryo-microscopy reveals an amphipol belt replacing the membrane lipid bilayer. A precise fit of the X-ray structures of complex I, the complex III dimer, and monomeric complex IV indicates distances of 13 nm between the ubiquinol-binding sites of complexes I and III, and of 10-11 nm between the cytochrome c binding sites of complexes III and IV. The arrangement of respiratory chain complexes suggests two possible pathways for efficient electron transfer through the supercomplex, of which the shorter branch through the complex III monomer proximal to complex I may be preferred. #1: Year: 2011 Title: Strukturelle Untersuchungen am Superkomplex I1III2IV1 der Atmungskette mittels Kryoelektronenmikroskopie Authors: Althoff T | |||||||||
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_1876.map.gz | 250.7 KB | EMDB map data format | |
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Header (meta data) | emd-1876-v30.xml emd-1876.xml | 20.2 KB 20.2 KB | Display Display | EMDB header |
Images | EMD1876_bt_mito_supercomplex-b_cryo_front-view.tif | 160.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1876 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1876 | HTTPS FTP |
-Validation report
Summary document | emd_1876_validation.pdf.gz | 198.1 KB | Display | EMDB validaton report |
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Full document | emd_1876_full_validation.pdf.gz | 197.2 KB | Display | |
Data in XML | emd_1876_validation.xml.gz | 5.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1876 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1876 | HTTPS FTP |
-Related structure data
Related structure data | 2ybbMC 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_1876.map.gz / Format: CCP4 / Size: 5.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D cryo-EM map of supercomplex B (I1III2IV1) from bovine heart mitochondria | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.76 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 : Respiratory supercomplex B (I1III2IV1) composed of complex I, dim...
Entire | Name: Respiratory supercomplex B (I1III2IV1) composed of complex I, dimeric complex III and complex IV from bovine heart mitochondria |
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Components |
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-Supramolecule #1000: Respiratory supercomplex B (I1III2IV1) composed of complex I, dim...
Supramolecule | Name: Respiratory supercomplex B (I1III2IV1) composed of complex I, dimeric complex III and complex IV from bovine heart mitochondria type: sample / ID: 1000 Details: The supercomplexes were kept soluble by amphipol A8-35 Oligomeric state: A monomer of complex I assembles with a dimer of complex III and a monomer of complex IV Number unique components: 4 |
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Molecular weight | Theoretical: 1.7 MDa |
-Macromolecule #1: NADH-dehydrogenase
Macromolecule | Name: NADH-dehydrogenase / type: protein_or_peptide / ID: 1 / Name.synonym: Complex I / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No |
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Source (natural) | Organism: Bos taurus (cattle) / synonym: Cattle / Tissue: Heart Muscle / Organelle: Mitochondrion / Location in cell: Inner mitochondrial membrane |
Molecular weight | Experimental: 980 KDa / Theoretical: 980 KDa |
-Macromolecule #2: Cytochrome c reductase
Macromolecule | Name: Cytochrome c reductase / type: protein_or_peptide / ID: 2 / Name.synonym: Complex III / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: No |
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Source (natural) | Organism: Bos taurus (cattle) / synonym: Cattle / Tissue: Heart Muscle / Organelle: Mitochondrion / Location in cell: Inner mitochondrial membrane |
Molecular weight | Experimental: 243 KDa / Theoretical: 241 KDa |
-Macromolecule #3: Cytochrome c oxidase
Macromolecule | Name: Cytochrome c oxidase / type: protein_or_peptide / ID: 3 / Name.synonym: Complex IV / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No |
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Source (natural) | Organism: Bos taurus (cattle) / synonym: Cattle / Tissue: Heart Muscle / Organelle: Mitochondrion / Location in cell: Inner mitochondrial membrane |
Molecular weight | Experimental: 207 KDa / Theoretical: 204 KDa |
-Macromolecule #4: Cytochrome c
Macromolecule | Name: Cytochrome c / type: protein_or_peptide / ID: 4 / Name.synonym: Cytochrome c / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No |
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Source (natural) | Organism: Bos taurus (cattle) / synonym: Cattle / Tissue: Heart Muscle / Organelle: Mitochondrion / Location in cell: Inner mitochondrial membrane |
Molecular weight | Experimental: 12 KDa / Theoretical: 12 KDa |