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- PDB-6ynz: Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP sy... -
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Basic information
Entry | Database: PDB / ID: 6ynz | ||||||||||||
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Title | Cryo-EM structure of Tetrahymena thermophila mitochondrial ATP synthase - F1Fo composite tetramer model | ||||||||||||
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![]() | MEMBRANE PROTEIN / mitochondria / ATP synthase / F1Fo tetramer | ||||||||||||
Function / homology | ![]() : / sulfide oxidation, using sulfide:quinone oxidoreductase / sulfide:quinone oxidoreductase activity / cellular lipid metabolic process / carboxylic ester hydrolase activity / : / : / : / : / proton-transporting ATP synthase complex, coupling factor F(o) ...: / sulfide oxidation, using sulfide:quinone oxidoreductase / sulfide:quinone oxidoreductase activity / cellular lipid metabolic process / carboxylic ester hydrolase activity / : / : / : / : / proton-transporting ATP synthase complex, coupling factor F(o) / photosynthetic electron transport in photosystem I / : / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / chloroplast thylakoid membrane / proton motive force-driven mitochondrial ATP synthesis / 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 / ADP binding / hydrolase activity / lipid binding / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
![]() | Kock Flygaard, R. / Muhleip, A. / Amunts, A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 11.3 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 10861MC ![]() 6ynvC ![]() 6ynwC ![]() 6ynxC ![]() 6ynyC ![]() 6yo0C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
+Protein , 25 types, 134 molecules aAa3A3bBb3B3dDd3D3fFf3F3iIi3I3kKk3K3cCc3C3gG...
-ATP synthase subunit ... , 3 types, 28 molecules g1g2g4g5C1B1A1C2B2A2C4B4A4C5B5A5D1F1E1D2F2E2D4F4E4D5F5E5
#23: Protein | Mass: 32915.152 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #24: Protein | Mass: 59744.012 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #25: Protein | Mass: 53490.848 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 9 types, 140 molecules ![](data/chem/img/CDL.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/UQ8.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PEE.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/UQ8.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PEE.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/ADP.gif)
#29: Chemical | ChemComp-CDL / #30: Chemical | ChemComp-PC1 / #31: Chemical | ChemComp-PO4 / #32: Chemical | ChemComp-UQ8 / #33: Chemical | ChemComp-ATP / #34: Chemical | ChemComp-MG / #35: Chemical | ChemComp-PEE / #36: Chemical | ChemComp-NAD / #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 |
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Sample preparation
Component | Name: Mitochondrial ATP synthase, F1Fo tetramer / Type: COMPLEX / Entity ID: #1-#28 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
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 |
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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: ![]() |
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 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | |||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40691 / Symmetry type: POINT |