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Yorodumi- EMDB-10861: Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP sy... -
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-Basic information
Entry | Database: EMDB / ID: EMD-10861 | ||||||||||||
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Title | Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP synthase - F1Fo tetramer | ||||||||||||
Map data | Local-resolution filtered full map of T. thermophila ATP synthase tetramer, Fo-subcomplexes masked | ||||||||||||
Sample |
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Function / homology | Function and homology information : / sulfide oxidation, using sulfide:quinone oxidoreductase / sulfide:quinone oxidoreductase activity / cellular lipid metabolic process / carboxylic ester hydrolase activity / : / : / : / : / photosynthetic electron transport in photosystem I ...: / sulfide oxidation, using sulfide:quinone oxidoreductase / sulfide:quinone oxidoreductase activity / cellular lipid metabolic process / carboxylic ester hydrolase activity / : / : / : / : / photosynthetic electron transport in photosystem I / proton-transporting ATP synthase complex, coupling factor F(o) / : / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / chloroplast thylakoid membrane / photosynthetic electron transport in photosystem II / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / FAD binding / proton-transporting ATP synthase activity, rotational mechanism / proton motive force-driven mitochondrial ATP synthesis / ADP binding / hydrolase activity / lipid binding / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Tetrahymena thermophila (eukaryote) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Kock Flygaard R / Muhleip A / Amunts A | ||||||||||||
Funding support | Sweden, 3 items
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Citation | Journal: Nat Commun / Year: 2020 Title: 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10861.map.gz | 468.7 MB | EMDB map data format | |
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Header (meta data) | emd-10861-v30.xml emd-10861.xml | 45.6 KB 45.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10861_fsc.xml | 21.2 KB | Display | FSC data file |
Images | emd_10861.png | 62.4 KB | ||
Masks | emd_10861_msk_1.map | 824 MB | Mask map | |
Others | emd_10861_half_map_1.map.gz emd_10861_half_map_2.map.gz | 665.7 MB 665.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10861 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10861 | HTTPS FTP |
-Validation report
Summary document | emd_10861_validation.pdf.gz | 460.3 KB | Display | EMDB validaton report |
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Full document | emd_10861_full_validation.pdf.gz | 459.4 KB | Display | |
Data in XML | emd_10861_validation.xml.gz | 24.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10861 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10861 | HTTPS FTP |
-Related structure data
Related structure data | 6ynzMC 6ynvC 6ynwC 6ynxC 6ynyC 6yo0C 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_10861.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 tetramer, Fo-subcomplexes masked | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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_10861_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half-map 1
File | emd_10861_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_10861_half_map_2.map | ||||||||||||
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Annotation | Half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Mitochondrial ATP synthase, F1Fo tetramer
+Supramolecule #1: Mitochondrial ATP synthase, F1Fo tetramer
+Macromolecule #1: Ymf66
+Macromolecule #2: subunit b
+Macromolecule #3: subunit d
+Macromolecule #4: subunit f
+Macromolecule #5: subunit i/j
+Macromolecule #6: subunit k
+Macromolecule #7: Ymf56
+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: ATP synthase subunit gamma
+Macromolecule #24: ATP synthase subunit alpha
+Macromolecule #25: ATP synthase subunit beta
+Macromolecule #26: ATP synthase F0 subunit 9
+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 |
-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 |
-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 |