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Yorodumi- EMDB-10860: Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP sy... -
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Basic information
| Entry | Database: EMDB / ID: EMD-10860 | ||||||||||||
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| Title | Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP synthase - F1Fo dimer | ||||||||||||
Map data | Local-resolution filtered full map of T. thermophila ATP synthase | ||||||||||||
Sample |
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Keywords | mitochondria / ATP synthase / F1Fo dimer / IF1 dimer / MEMBRANE PROTEIN | ||||||||||||
| Function / homology | Function and homology information: / sulfide oxidation, using sulfide:quinone oxidoreductase / sulfide:quinone oxidoreductase activity / thylakoid / carboxylic ester hydrolase activity / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton motive force-driven mitochondrial ATP synthesis / H+-transporting two-sector ATPase ...: / sulfide oxidation, using sulfide:quinone oxidoreductase / sulfide:quinone oxidoreductase activity / thylakoid / carboxylic ester hydrolase activity / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton motive force-driven mitochondrial ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / FAD binding / ADP binding / hydrolase activity / mitochondrial inner membrane / lipid binding / ATP hydrolysis activity / mitochondrion / ATP binding / membrane Similarity search - Function | ||||||||||||
| Biological species | ![]() | ||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||||||||
Authors | Kock Flygaard R / Muhleip A | ||||||||||||
| Funding support | Sweden, 3 items
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Citation | Journal: Nat Commun / Year: 2020Title: Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization. Authors: Rasmus Kock Flygaard / Alexander Mühleip / Victor Tobiasson / Alexey Amunts / ![]() Abstract: Mitochondrial ATP synthases form functional homodimers to induce cristae curvature that is a universal property of mitochondria. To expand on the understanding of this fundamental phenomenon, we ...Mitochondrial ATP synthases form functional homodimers to induce cristae curvature that is a universal property of mitochondria. To expand on the understanding of this fundamental phenomenon, we characterized the unique type III mitochondrial ATP synthase in its dimeric and tetrameric form. The cryo-EM structure of a ciliate ATP synthase dimer reveals an unusual U-shaped assembly of 81 proteins, including a substoichiometrically bound ATPTT2, 40 lipids, and co-factors NAD and CoQ. A single copy of subunit ATPTT2 functions as a membrane anchor for the dimeric inhibitor IF. Type III specific linker proteins stably tie the ATP synthase monomers in parallel to each other. The intricate dimer architecture is scaffolded by an extended subunit-a that provides a template for both intra- and inter-dimer interactions. The latter results in the formation of tetramer assemblies, the membrane part of which we determined to 3.1 Å resolution. The structure of the type III ATP synthase tetramer and its associated lipids suggests that it is the intact unit propagating the membrane curvature. | ||||||||||||
| History |
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Structure visualization
| Movie |
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| Structure viewer | EM map: SurfView Molmil Jmol/JSmol |
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_10860.map.gz | 473.9 MB | EMDB map data format | |
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| Header (meta data) | emd-10860-v30.xml emd-10860.xml | 56.4 KB 56.4 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_10860_fsc.xml | 21.1 KB | Display | FSC data file |
| Images | emd_10860.png | 81.6 KB | ||
| Masks | emd_10860_msk_1.map | 824 MB | Mask map | |
| Filedesc metadata | emd-10860.cif.gz | 13.2 KB | ||
| Others | emd_10860_half_map_1.map.gz emd_10860_half_map_2.map.gz | 673.3 MB 670.7 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10860 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10860 | HTTPS FTP |
-Validation report
| Summary document | emd_10860_validation.pdf.gz | 988.1 KB | Display | EMDB validaton report |
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| Full document | emd_10860_full_validation.pdf.gz | 987.7 KB | Display | |
| Data in XML | emd_10860_validation.xml.gz | 27.8 KB | Display | |
| Data in CIF | emd_10860_validation.cif.gz | 36.9 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10860 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10860 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 6ynyMC ![]() 6ynvC ![]() 6ynwC ![]() 6ynxC ![]() 6ynzC ![]() 6yo0C M: atomic model generated by this map C: citing same article ( |
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| Similar structure data |
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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_10860.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| Annotation | Local-resolution filtered full map of T. thermophila ATP synthase | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
| File | emd_10860_msk_1.map | ||||||||||||
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| Density Histograms |
-Half map: Half-map 1
| File | emd_10860_half_map_1.map | ||||||||||||
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| Annotation | Half-map 1 | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: Half-map 2
| File | emd_10860_half_map_2.map | ||||||||||||
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| Annotation | Half-map 2 | ||||||||||||
| Projections & Slices |
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| Density Histograms |
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Sample components
+Entire : Mitochondrial ATP synthase, F1Fo dimer
+Supramolecule #1: Mitochondrial ATP synthase, F1Fo dimer
+Macromolecule #1: subunit a
+Macromolecule #2: subunit b
+Macromolecule #3: subunit d
+Macromolecule #4: subunit f
+Macromolecule #5: subunit i/j
+Macromolecule #6: subunit k
+Macromolecule #7: subunit 8
+Macromolecule #8: ATPTT3
+Macromolecule #9: ATPTT4
+Macromolecule #10: ATPTT5
+Macromolecule #11: ATPTT6
+Macromolecule #12: ATPTT7
+Macromolecule #13: ATPTT8
+Macromolecule #14: ATPTT9
+Macromolecule #15: ATPTT10
+Macromolecule #16: ATPTT11
+Macromolecule #17: ATPTT12
+Macromolecule #18: ATPTT13
+Macromolecule #19: ATPTT1
+Macromolecule #20: Inhibitor of F1 (IF1)
+Macromolecule #21: ATPTT2
+Macromolecule #22: Oligomycin sensitivity-conferring protein (OSCP)
+Macromolecule #23: subunit gamma
+Macromolecule #24: subunit alpha
+Macromolecule #25: subunit beta
+Macromolecule #26: subunit c
+Macromolecule #27: subunit delta
+Macromolecule #28: subunit epsilon
+Macromolecule #29: CARDIOLIPIN
+Macromolecule #30: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #31: PHOSPHATE ION
+Macromolecule #32: Ubiquinone-8
+Macromolecule #33: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #34: MAGNESIUM ION
+Macromolecule #35: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
+Macromolecule #36: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
+Macromolecule #37: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Concentration | 0.75 mg/mL |
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| Buffer | pH: 7.5 |
| Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 |
| Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
| Microscope | FEI TITAN KRIOS |
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| Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
| Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.9 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 165000 |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Sweden, 3 items
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