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Yorodumi- EMDB-0262: III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0262 | |||||||||
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Title | III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae | |||||||||
Map data | The sharpened map of the III2IV2 supercomplex | |||||||||
Sample |
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Function / homology | Function and homology information matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial cytochrome c oxidase assembly / mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respirasome assembly / Mitochondrial protein degradation / : / : / cytochrome-c oxidase ...matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial cytochrome c oxidase assembly / mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respirasome assembly / Mitochondrial protein degradation / : / : / cytochrome-c oxidase / : / quinol-cytochrome-c reductase / cellular respiration / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / electron transport coupled proton transport / enzyme regulator activity / ATP synthesis coupled electron transport / proton transmembrane transport / nuclear periphery / mitochondrial membrane / aerobic respiration / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / mitochondrial inner membrane / copper ion binding / heme binding / mitochondrion / proteolysis / zinc ion binding / membrane / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.31 Å | |||||||||
Authors | Hartley AM / Lukoyanova N / Pinotsis N / Marechal A | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2019 Title: Structure of yeast cytochrome c oxidase in a supercomplex with cytochrome bc. Authors: Andrew M Hartley / Natalya Lukoyanova / Yunyi Zhang / Alfredo Cabrera-Orefice / Susanne Arnold / Brigitte Meunier / Nikos Pinotsis / Amandine Maréchal / Abstract: Cytochrome c oxidase (complex IV, CIV) is known in mammals to exist independently or in association with other respiratory proteins to form supercomplexes (SCs). In Saccharomyces cerevisiae, CIV is ...Cytochrome c oxidase (complex IV, CIV) is known in mammals to exist independently or in association with other respiratory proteins to form supercomplexes (SCs). In Saccharomyces cerevisiae, CIV is found solely in an SC with cytochrome bc (complex III, CIII). Here, we present the cryogenic electron microscopy (cryo-EM) structure of S. cerevisiae CIV in a IIIIV SC at 3.3 Å resolution. While overall similarity to mammalian homologs is high, we found notable differences in the supernumerary subunits Cox26 and Cox13; the latter exhibits a unique arrangement that precludes CIV dimerization as seen in bovine. A conformational shift in the matrix domain of Cox5A-involved in allosteric inhibition by ATP-may arise from its association with CIII. The CIII-CIV arrangement highlights a conserved interaction interface of CIII, albeit one occupied by complex I in mammalian respirasomes. We discuss our findings in the context of the potential impact of SC formation on CIV regulation. | |||||||||
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_0262.map.gz | 106.3 MB | EMDB map data format | |
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Header (meta data) | emd-0262-v30.xml emd-0262.xml | 30.6 KB 30.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0262_fsc.xml | 11 KB | Display | FSC data file |
Images | emd_0262.png | 147.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0262 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0262 | HTTPS FTP |
-Validation report
Summary document | emd_0262_validation.pdf.gz | 335.7 KB | Display | EMDB validaton report |
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Full document | emd_0262_full_validation.pdf.gz | 334.8 KB | Display | |
Data in XML | emd_0262_validation.xml.gz | 11.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0262 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0262 | HTTPS FTP |
-Related structure data
Related structure data | 6hu9MC 0268C 0269C 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_0262.map.gz / Format: CCP4 / Size: 113.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The sharpened map of the III2IV2 supercomplex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3861 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 : III2-IV2 mitochondrial respiratory supercomplex
+Supramolecule #1: III2-IV2 mitochondrial respiratory supercomplex
+Supramolecule #2: 10-subunit yeast cytochrome bc1
+Supramolecule #3: 12-subunit cytochrome c oxidase with isoform Cox5A
+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 6
+Macromolecule #7: Cytochrome b-c1 complex subunit 7
+Macromolecule #8: Cytochrome b-c1 complex subunit 8
+Macromolecule #9: Cytochrome b-c1 complex subunit 9
+Macromolecule #10: Cytochrome b-c1 complex subunit 10
+Macromolecule #11: Cox1
+Macromolecule #12: Cox2
+Macromolecule #13: Cox3
+Macromolecule #14: Cox4
+Macromolecule #15: Cox5A
+Macromolecule #16: Cox6
+Macromolecule #17: Cox7
+Macromolecule #18: Cox8
+Macromolecule #19: Cox9
+Macromolecule #20: Cox12
+Macromolecule #21: Cox13
+Macromolecule #22: Cox26
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 4.0 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 92 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV Details: 3 uL of sample applied to negatively glow discharged grid, blot force -10; blotting time 8.5 sec. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Sampling interval: 5.0 µm / Average exposure time: 8.0 sec. / Average electron dose: 1.645 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 130000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |