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Yorodumi- PDB-6yny: Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP sy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yny | ||||||||||||
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Title | Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP synthase - F1Fo composite dimer model | ||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / mitochondria / ATP synthase / F1Fo dimer / IF1 dimer | ||||||||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||||||||
Authors | Kock Flygaard, R. / Muhleip, A. / Amunts, A. | ||||||||||||
Funding support | Sweden, 3items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6yny.cif.gz | 5.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6yny.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6yny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yny_validation.pdf.gz | 3.9 MB | Display | wwPDB validaton report |
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Full document | 6yny_full_validation.pdf.gz | 4.1 MB | Display | |
Data in XML | 6yny_validation.xml.gz | 388.1 KB | Display | |
Data in CIF | 6yny_validation.cif.gz | 614.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/6yny ftp://data.pdbj.org/pub/pdb/validation_reports/yn/6yny | HTTPS FTP |
-Related structure data
Related structure data | 10860MC 6ynvC 6ynwC 6ynxC 6ynzC 6yo0C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+Protein , 28 types, 81 molecules aAbBdDfFiIkKcCgGhHjJlLmMnNoOpP...
-Non-polymers , 9 types, 70 molecules
#29: Chemical | ChemComp-CDL / #30: Chemical | ChemComp-PC1 / #31: Chemical | #32: Chemical | #33: Chemical | ChemComp-ATP / #34: Chemical | ChemComp-MG / #35: Chemical | ChemComp-PEE / #36: Chemical | #37: Chemical | ChemComp-ADP / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Mitochondrial ATP synthase, F1Fo dimer / Type: COMPLEX / Entity ID: #1-#28 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Tetrahymena thermophila (eukaryote) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X |
Image recording | Electron dose: 30.9 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 20 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61157 / Symmetry type: POINT |