+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0005 | |||||||||
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Title | Saccharomyces cerevisiae supercomplex class 1 (III2IV) | |||||||||
Map data | Saccharomyces cerevisiae Class1 (III2IV) | |||||||||
Sample |
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Biological species | Saccharomyces cerevisiae W303 (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.34 Å | |||||||||
Authors | Rathore S / Berndtsson J / Conrad J / Ott M | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2019 Title: Cryo-EM structure of the yeast respiratory supercomplex. Authors: Sorbhi Rathore / Jens Berndtsson / Lorena Marin-Buera / Julian Conrad / Marta Carroni / Peter Brzezinski / Martin Ott / Abstract: Respiratory chain complexes execute energy conversion by connecting electron transport with proton translocation over the inner mitochondrial membrane to fuel ATP synthesis. Notably, these complexes ...Respiratory chain complexes execute energy conversion by connecting electron transport with proton translocation over the inner mitochondrial membrane to fuel ATP synthesis. Notably, these complexes form multi-enzyme assemblies known as respiratory supercomplexes. Here we used single-particle cryo-EM to determine the structures of the yeast mitochondrial respiratory supercomplexes IIIIV and IIIIV, at 3.2-Å and 3.5-Å resolutions, respectively. We revealed the overall architecture of the supercomplex, which deviates from the previously determined assemblies in mammals; obtained a near-atomic structure of the yeast complex IV; and identified the protein-protein and protein-lipid interactions implicated in supercomplex formation. Take together, our results demonstrate convergent evolution of supercomplexes in mitochondria that, while building similar assemblies, results in substantially different arrangements and structural solutions to support energy conversion. | |||||||||
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_0005.map.gz | 170.5 MB | EMDB map data format | |
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Header (meta data) | emd-0005-v30.xml emd-0005.xml | 19.7 KB 19.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0005_fsc.xml | 15.4 KB | Display | FSC data file |
Images | emd_0005.png | 264 KB | ||
Others | emd_0005_half_map_1.map.gz emd_0005_half_map_2.map.gz | 167.4 MB 167.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0005 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0005 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0005.map.gz / Format: CCP4 / Size: 193.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Saccharomyces cerevisiae Class1 (III2IV) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Halfmap1 class1
File | emd_0005_half_map_1.map | ||||||||||||
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Annotation | Halfmap1 class1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Halfmap2 class1
File | emd_0005_half_map_2.map | ||||||||||||
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Annotation | Halfmap2 class1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Saccharomyces cerevisiae Supercomplex (III2IV)
Entire | Name: Saccharomyces cerevisiae Supercomplex (III2IV) |
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Components |
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-Supramolecule #1: Saccharomyces cerevisiae Supercomplex (III2IV)
Supramolecule | Name: Saccharomyces cerevisiae Supercomplex (III2IV) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#25 |
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Source (natural) | Organism: Saccharomyces cerevisiae W303 (yeast) / Organelle: Mitochondria |
-Supramolecule #2: Saccharomyces cerevisiae complex III
Supramolecule | Name: Saccharomyces cerevisiae complex III / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#13 |
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Source (natural) | Organism: Saccharomyces cerevisiae W303 (yeast) / Organelle: Mitochondria |
-Supramolecule #3: Saccharomyces cerevisiae complex IV
Supramolecule | Name: Saccharomyces cerevisiae complex IV / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #14-#25 |
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Source (natural) | Organism: Saccharomyces cerevisiae W303 (yeast) / Organelle: Mitochondria |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |