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Yorodumi- PDB-6te0: Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6te0 | ||||||
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Title | Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase, OSCP/F1/c-ring, rotational state 3 | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / mitochondria / ATP synthase | ||||||
Function / homology | Function and homology information F1F0 ATP synthase subunit C / F1FO ATP Synthase / Thrombin, subunit H - #170 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Beta Barrel / Rossmann fold ...F1F0 ATP synthase subunit C / F1FO ATP Synthase / Thrombin, subunit H - #170 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Euglena gracilis (euglena) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.92 Å | ||||||
Authors | Muhleip, A. / Amunts, A. | ||||||
Citation | Journal: Elife / Year: 2019 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. | ||||||
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 | 6te0.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6te0.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 6te0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6te0_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6te0_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6te0_validation.xml.gz | 129.8 KB | Display | |
Data in CIF | 6te0_validation.cif.gz | 201.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/6te0 ftp://data.pdbj.org/pub/pdb/validation_reports/te/6te0 | HTTPS FTP |
-Related structure data
Related structure data | 10473MC 6tduC 6tdvC 6tdwC 6tdxC 6tdyC 6tdzC 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
-ATP synthase subunit ... , 5 types, 18 molecules CABFDEHIOPQRSTUVWX
#1: Protein | Mass: 61897.199 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) #2: Protein | Mass: 53213.035 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) #6: Protein | | Mass: 19559.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) #7: Protein | | Mass: 8751.981 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) #8: Protein | Mass: 10820.831 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) |
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-Protein , 3 types, 5 molecules LJKMG
#3: Protein | Mass: 20995.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) #4: Protein | | Mass: 29564.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) #5: Protein | | Mass: 35110.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) |
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-Non-polymers , 4 types, 11 molecules
#9: Chemical | ChemComp-ATP / #10: Chemical | ChemComp-MG / #11: Chemical | ChemComp-ADP / | #12: Chemical | ChemComp-TRT / | |
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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 |
-Sample preparation
Component | Name: mitochondrial ATP synthase dimer of Euglena gracilis / Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL |
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Molecular weight | Value: 2 MDa / Experimental value: NO |
Source (natural) | Organism: Euglena gracilis (euglena) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 5 seconds blot |
-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: 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 |
-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: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Resolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43232 / Algorithm: FOURIER SPACE / Symmetry type: POINT |