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Yorodumi- EMDB-10862: Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP sy... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10862 | ||||||||||||
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Title | Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP synthase - F1/peripheral stalk | ||||||||||||
Map data | Local-resolution filtered full map of T. thermophila ATP synthase F1/peripheral stalk | ||||||||||||
Sample |
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Function / homology | Function and homology information thylakoid / : / : / : / : / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase ...thylakoid / : / : / : / : / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / chloroplast / ADP binding / ATP hydrolysis activity / ATP binding / membrane Similarity search - Function | ||||||||||||
Biological species | Tetrahymena thermophila (eukaryote) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 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_10862.map.gz | 473.2 MB | EMDB map data format | |
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Header (meta data) | emd-10862-v30.xml emd-10862.xml | 24.2 KB 24.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10862_fsc.xml | 21.1 KB | Display | FSC data file |
Images | emd_10862.png | 80.3 KB | ||
Masks | emd_10862_msk_1.map | 824 MB | Mask map | |
Others | emd_10862_half_map_1.map.gz emd_10862_half_map_2.map.gz | 672.4 MB 671.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10862 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10862 | HTTPS FTP |
-Validation report
Summary document | emd_10862_validation.pdf.gz | 377.1 KB | Display | EMDB validaton report |
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Full document | emd_10862_full_validation.pdf.gz | 376.3 KB | Display | |
Data in XML | emd_10862_validation.xml.gz | 25 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10862 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10862 | HTTPS FTP |
-Related structure data
Related structure data | 6yo0MC 6ynvC 6ynwC 6ynxC 6ynyC 6ynzC 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_10862.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 F1/peripheral stalk | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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_10862_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half-map 1
File | emd_10862_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_10862_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, F1/peripheral stalk
+Supramolecule #1: Mitochondrial ATP synthase, F1/peripheral stalk
+Macromolecule #1: Oligomycin sensitivity-conferring protein (OSCP)
+Macromolecule #2: ATP synthase subunit gamma
+Macromolecule #3: ATP synthase subunit alpha
+Macromolecule #4: ATP synthase subunit beta
+Macromolecule #5: Inhibitor of F1 (IF1)
+Macromolecule #6: ATPTT13
+Macromolecule #7: subunit b
+Macromolecule #8: subunit d
+Macromolecule #9: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #10: MAGNESIUM ION
+Macromolecule #11: 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 |