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- PDB-6tdu: Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase,... -
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Basic information
Entry | Database: PDB / ID: 6tdu | ||||||
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Title | Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase, full dimer, rotational states 1 | ||||||
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![]() | MEMBRANE PROTEIN / mitochondria / ATP synthase | ||||||
Function / homology | ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / CARDIOLIPIN / Chem-LPP![]() | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.32 Å | ||||||
![]() | Muhleip, A. / Amunts, A. | ||||||
![]() | ![]() Title: Structure of a mitochondrial ATP synthase with bound native cardiolipin. Authors: Alexander Mühleip / Sarah E McComas / Alexey Amunts / ![]() Abstract: The mitochondrial ATP synthase fuels eukaryotic cells with chemical energy. Here we report the cryo-EM structure of a divergent ATP synthase dimer from mitochondria of , a member of the phylum ...The mitochondrial ATP synthase fuels eukaryotic cells with chemical energy. Here we report the cryo-EM structure of a divergent ATP synthase dimer from mitochondria of , a member of the phylum Euglenozoa that also includes human parasites. It features 29 different subunits, 8 of which are newly identified. The membrane region was determined to 2.8 Å resolution, enabling the identification of 37 associated lipids, including 25 cardiolipins, which provides insight into protein-lipid interactions and their functional roles. The rotor-stator interface comprises four membrane-embedded horizontal helices, including a distinct subunit . The dimer interface is formed entirely by phylum-specific components, and a peripherally associated subcomplex contributes to the membrane curvature. The central and peripheral stalks directly interact with each other. Last, the ATPase inhibitory factor 1 (IF) binds in a mode that is different from human, but conserved in Trypanosomatids. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 5.4 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 4.9 MB | Display | ![]() |
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Full document | ![]() | 5 MB | Display | |
Data in XML | ![]() | 416.2 KB | Display | |
Data in CIF | ![]() | 624 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 10467MC ![]() 6tdvC ![]() 6tdwC ![]() 6tdxC ![]() 6tdyC ![]() 6tdzC ![]() 6te0C 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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1 |
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Components
-Protein , 16 types, 36 molecules AaDdEeMmNnOoPpQqRrSsTtAJAKALBJBKBLAMBM...
#1: Protein | Mass: 56026.699 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 21737.113 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 11432.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #11: Protein | Mass: 19738.803 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #12: Protein | Mass: 16210.519 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #13: Protein | Mass: 13807.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #14: Protein | Mass: 13703.778 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #15: Protein | Mass: 10825.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #16: Protein | Mass: 9236.822 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #17: Protein | Mass: 8861.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #18: Protein | Mass: 7441.788 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #24: Protein | Mass: 20995.094 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() #25: Protein | Mass: 29564.520 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #26: Protein | Mass: 11687.415 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #28: Protein | Mass: 35175.836 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #29: Protein | Mass: 18833.510 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-ATP synthase subunit ... , 13 types, 52 molecules FfGgHhIiJjKkLlAAABACBABBBCADAEAFBDBEBFAGBGAHBH...
#4: Protein | Mass: 32666.373 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | Mass: 12673.109 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #6: Protein | Mass: 53928.289 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein | Mass: 11193.877 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #8: Protein | Mass: 12529.404 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #9: Protein | Mass: 12739.871 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #10: Protein | Mass: 7011.208 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #19: Protein | Mass: 61897.199 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() #20: Protein | Mass: 53991.066 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() #21: Protein | Mass: 35110.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #22: Protein | Mass: 19559.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #23: Protein | Mass: 8751.981 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #27: Protein | Mass: 10820.831 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Sugars , 1 types, 8 molecules ![](data/chem/img/LMT.gif)
#31: Sugar | ChemComp-LMT / |
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-Non-polymers , 6 types, 75 molecules ![](data/chem/img/CDL.gif)
![](data/chem/img/LPP.gif)
![](data/chem/img/TRT.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/LPP.gif)
![](data/chem/img/TRT.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
#30: Chemical | ChemComp-CDL / #32: Chemical | ChemComp-LPP / #33: Chemical | ChemComp-TRT / #34: Chemical | ChemComp-ATP / #35: Chemical | ChemComp-MG / #36: Chemical | |
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-Details
Has ligand of interest | Y |
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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: Euglena gracilis mitochondrial ATP synthase dimer / Type: COMPLEX / Entity ID: #1-#29 / Source: NATURAL |
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Molecular weight | Value: 2 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.4 |
Specimen | 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 R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 3 seconds blot |
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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: 130000 X / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 36.3 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of real images: 9045 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||
Particle selection | Num. of particles selected: 555269 | ||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||
3D reconstruction | Resolution: 4.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27232 / Algorithm: FOURIER SPACE / Symmetry type: POINT |