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Yorodumi- EMDB-65584: Cryo-EM structure of complex III on the bovine heart submitochond... -
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Basic information
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| Title | Cryo-EM structure of complex III on the bovine heart submitochondrial particles, III-2 | ||||||||||||
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Keywords | respiratory chain complex / supercomplex / submitochondrial particles / MOTOR PROTEIN / OXIDOREDUCTASE | ||||||||||||
| Function / homology | Function and homology informationComplex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / Respiratory electron transport / thalamus development / Mitochondrial translation termination / respiratory chain complex III / quinol-cytochrome-c reductase ...Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / Respiratory electron transport / thalamus development / Mitochondrial translation termination / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / hypothalamus development / midbrain development / ubiquinone binding / respiratory electron transport chain / hippocampus development / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial membrane / oxidoreductase activity / mitochondrial inner membrane / heme binding / protein-containing complex / mitochondrion / proteolysis / membrane / metal ion binding Similarity search - Function | ||||||||||||
| Biological species | ![]() | ||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.4 Å | ||||||||||||
Authors | Nakano A / Masuya T / Akisada S / Ishikawa-Fukuda M / Mitsuoka K / Miyoshi H / Murai M / Yokoyama K | ||||||||||||
| Funding support | Japan, 3 items
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Citation | Journal: Nat Commun / Year: 2026Title: Structures of respiratory supercomplexes and ATP synthase oligomers in mammalian mitochondrial inner membrane. Authors: Atsuki Nakano / Takahiro Masuya / Shinsuke Akisada / Moe Ishikawa-Fukuda / Kaoru Mitsuoka / Hideto Miyoshi / Masatoshi Murai / Ken Yokoyama / ![]() Abstract: Understanding the functional mechanisms of membrane protein complexes requires structural analysis within their native membrane environment. Here, we applied cryo-electron microscopy to determine the ...Understanding the functional mechanisms of membrane protein complexes requires structural analysis within their native membrane environment. Here, we applied cryo-electron microscopy to determine the structures of FF ATP synthase and respiratory supercomplexes (SCs) on sub-mitochondrial particles (SMPs) isolated from bovine heart mitochondria. Most FF complexes were observed as dimers stabilized by the regulatory factor IF₁, and a tetrameric assembly comprising two FF-IF₁ dimers arranged linearly was also identified. This finding indicates that the tetrameric units of FF are present in the mitochondrial inner membrane and contribute to shaping cristae tips in mammalian mitochondria. F domain maps resolve the e-subunit- c₈-ring interface and show no discrete density for a tightly bound lipid within the c₈-ring. In addition to the previously reported SCs compositions CI₁CIII₂CIV₁ and CI₁CIII₂CIV₂, our analysis identified an additional assembly with the composition CI₁CIII₂CIV₃, as well as a CI₂CIII₂CIV₆ mega-complex. This approach enables rapid structural determination of FF ATP synthase and SCs from minimal membrane fractions, providing a foundation for elucidating the molecular basis of metabolic disorders and mitochondrial diseases at the level of higher-order architecture. | ||||||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_65584.map.gz | 415.3 MB | EMDB map data format | |
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| Header (meta data) | emd-65584-v30.xml emd-65584.xml | 32.9 KB 32.9 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_65584_fsc.xml | 19.7 KB | Display | FSC data file |
| Images | emd_65584.png | 82.4 KB | ||
| Masks | emd_65584_msk_1.map | 824 MB | Mask map | |
| Filedesc metadata | emd-65584.cif.gz | 8 KB | ||
| Others | emd_65584_additional_1.map.gz emd_65584_half_map_1.map.gz emd_65584_half_map_2.map.gz | 778.3 MB 765.6 MB 765.6 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-65584 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-65584 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9w2yMC ![]() 9w2rC ![]() 9w2sC ![]() 9w2tC ![]() 9w2uC ![]() 9w2vC ![]() 9w2xC ![]() 9w2zC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_65584.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
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| Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Mask #1
| File | emd_65584_msk_1.map | ||||||||||||
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-Additional map: #1
| File | emd_65584_additional_1.map | ||||||||||||
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-Half map: #1
| File | emd_65584_half_map_1.map | ||||||||||||
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-Half map: #2
| File | emd_65584_half_map_2.map | ||||||||||||
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Sample components
+Entire : Complex III on the bovine heart submitochondrial particles
+Supramolecule #1: Complex III on the bovine heart submitochondrial particles
+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 7
+Macromolecule #7: Cytochrome b-c1 complex subunit 8
+Macromolecule #8: Cytochrome b-c1 complex subunit 6, mitochondrial
+Macromolecule #9: Cytochrome b-c1 complex subunit 9
+Macromolecule #10: Cytochrome b-c1 complex subunit 9
+Macromolecule #11: Cytochrome b-c1 complex subunit 10
+Macromolecule #12: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #13: HEME C
+Macromolecule #14: FE2/S2 (INORGANIC) CLUSTER
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.5 |
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| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Authors
Japan, 3 items
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Processing
FIELD EMISSION GUN


