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Yorodumi- EMDB-65581: Cryo-EM structure of complex I on the bovine heart submitochondri... -
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Basic information
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| Title | Cryo-EM structure of complex I on the bovine heart submitochondrial particles, closed | ||||||||||||
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Keywords | respiratory chain complex / supercomplex / submitochondrial particles / MOTOR PROTEIN / OXIDOREDUCTASE | ||||||||||||
| Function / homology | Function and homology informationComplex I biogenesis / Mitochondrial protein import / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / RHOG GTPase cycle / Complex I biogenesis / Mitochondrial ribosome-associated quality control / Complex I biogenesis / Respiratory electron transport / Respiratory electron transport ...Complex I biogenesis / Mitochondrial protein import / Protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / RHOG GTPase cycle / Complex I biogenesis / Mitochondrial ribosome-associated quality control / Complex I biogenesis / Respiratory electron transport / Respiratory electron transport / NADH dehydrogenase complex / Respiratory electron transport / protein lipoylation / cellular response to oxygen levels / iron-sulfur cluster assembly complex / ubiquinone biosynthetic process / mitochondrial large ribosomal subunit binding / mitochondrial [2Fe-2S] assembly complex / gliogenesis / Mitochondrial translation termination / Neutrophil degranulation / neural precursor cell proliferation / [2Fe-2S] cluster assembly / oxygen sensor activity / iron-sulfur cluster assembly / Mitochondrial protein degradation / NADH:ubiquinone reductase (H+-translocating) / ubiquinone binding / mitochondrial ATP synthesis coupled electron transport / electron transport coupled proton transport / proton motive force-driven mitochondrial ATP synthesis / mitochondrial electron transport, NADH to ubiquinone / acyl binding / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase activity / oxidoreductase activity, acting on NAD(P)H / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / response to cAMP / acyl carrier activity / quinone binding / ATP synthesis coupled electron transport / reactive oxygen species metabolic process / Mitochondrial protein degradation / neurogenesis / aerobic respiration / fatty acid binding / respiratory electron transport chain / electron transport chain / circadian rhythm / brain development / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / mitochondrial membrane / NAD binding / fatty acid biosynthetic process / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / mitochondrial inner membrane / mitochondrial matrix / negative regulation of DNA-templated transcription / apoptotic process / protein-containing complex binding / structural molecule activity / mitochondrion / RNA binding / nucleoplasm / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||
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| Method | single particle reconstruction / cryo EM / Resolution: 2.8 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_65581.map.gz | 416.4 MB | EMDB map data format | |
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| Header (meta data) | emd-65581-v30.xml emd-65581.xml | 78.2 KB 78.2 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_65581_fsc.xml | 19.7 KB | Display | FSC data file |
| Images | emd_65581.png | 80.7 KB | ||
| Masks | emd_65581_msk_1.map | 824 MB | Mask map | |
| Filedesc metadata | emd-65581.cif.gz | 14.7 KB | ||
| Others | emd_65581_additional_1.map.gz emd_65581_half_map_1.map.gz emd_65581_half_map_2.map.gz | 778.4 MB 765.1 MB 765.2 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-65581 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-65581 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9w2vMC ![]() 9w2rC ![]() 9w2sC ![]() 9w2tC ![]() 9w2uC ![]() 9w2xC ![]() 9w2yC ![]() 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_65581.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_65581_msk_1.map | ||||||||||||
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-Additional map: #1
| File | emd_65581_additional_1.map | ||||||||||||
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-Half map: #2
| File | emd_65581_half_map_1.map | ||||||||||||
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| File | emd_65581_half_map_2.map | ||||||||||||
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Sample components
+Entire : Complex I on the bovine heart submitochondrial particles
+Supramolecule #1: Complex I on the bovine heart submitochondrial particles
+Macromolecule #1: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #2: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+Macromolecule #3: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+Macromolecule #4: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+Macromolecule #5: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+Macromolecule #6: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #7: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+Macromolecule #8: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #9: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+Macromolecule #10: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #11: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #12: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #13: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #14: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #15: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #16: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+Macromolecule #17: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #18: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #19: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #20: Acyl carrier protein, mitochondrial
+Macromolecule #21: Acyl carrier protein, mitochondrial
+Macromolecule #22: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+Macromolecule #23: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #24: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #25: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+Macromolecule #26: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #28: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+Macromolecule #29: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+Macromolecule #30: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #31: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #32: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+Macromolecule #33: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+Macromolecule #34: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+Macromolecule #35: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+Macromolecule #36: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+Macromolecule #37: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #39: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+Macromolecule #40: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #41: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #42: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+Macromolecule #43: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #44: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+Macromolecule #45: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+Macromolecule #46: N-FORMYLMETHIONINE
+Macromolecule #47: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #48: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #49: IRON/SULFUR CLUSTER
+Macromolecule #50: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #51: FLAVIN MONONUCLEOTIDE
+Macromolecule #52: POTASSIUM ION
+Macromolecule #53: CARDIOLIPIN
+Macromolecule #54: MAGNESIUM ION
+Macromolecule #55: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #56: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #57: ZINC ION
-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: 1.8 µm / Nominal defocus min: 0.8 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Keywords
Authors
Japan, 3 items
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Processing
FIELD EMISSION GUN


