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- PDB-6rdi: Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rdi | |||||||||
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Title | Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1A, monomer-masked refinement | |||||||||
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![]() | PROTON TRANSPORT / mitochondrial ATP synthase dimer flexible coupling cryoEM | |||||||||
Function / homology | ![]() thylakoid / : / : / : / : / 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 ...thylakoid / : / : / : / : / 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 / 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 / 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: 3.2 Å | |||||||||
![]() | Murphy, B.J. / Klusch, N. / Yildiz, O. / Kuhlbrandt, W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Rotary substates of mitochondrial ATP synthase reveal the basis of flexible F-F coupling. Authors: Bonnie J Murphy / Niklas Klusch / Julian Langer / Deryck J Mills / Özkan Yildiz / Werner Kühlbrandt / ![]() Abstract: FF-adenosine triphosphate (ATP) synthases make the energy of the proton-motive force available for energy-consuming processes in the cell. We determined the single-particle cryo-electron microscopy ...FF-adenosine triphosphate (ATP) synthases make the energy of the proton-motive force available for energy-consuming processes in the cell. We determined the single-particle cryo-electron microscopy structure of active dimeric ATP synthase from mitochondria of sp. at a resolution of 2.7 to 2.8 angstroms. Separation of 13 well-defined rotary substates by three-dimensional classification provides a detailed picture of the molecular motions that accompany -ring rotation and result in ATP synthesis. Crucially, the F head rotates along with the central stalk and -ring rotor for the first ~30° of each 120° primary rotary step to facilitate flexible coupling of the stoichiometrically mismatched F and F subcomplexes. Flexibility is mediated primarily by the interdomain hinge of the conserved OSCP subunit. A conserved metal ion in the proton access channel may synchronize -ring protonation with rotation. | |||||||||
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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Download
PDBx/mmCIF format | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 966.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4819MC ![]() 4805C ![]() 4806C ![]() 4807C ![]() 4808C ![]() 4809C ![]() 4810C ![]() 4811C ![]() 4812C ![]() 4813C ![]() 4814C ![]() 4815C ![]() 4816C ![]() 4817C ![]() 4818C ![]() 4820C ![]() 4821C ![]() 4822C ![]() 4823C ![]() 4824C ![]() 4825C ![]() 4826C ![]() 4827C ![]() 4828C ![]() 4829C ![]() 4830C ![]() 4831C ![]() 4832C ![]() 4833C ![]() 4834C ![]() 4835C ![]() 4836C ![]() 4837C ![]() 4838C ![]() 4839C ![]() 4840C ![]() 4841C ![]() 4842C ![]() 4843C ![]() 4844C ![]() 4845C ![]() 4846C ![]() 4847C ![]() 4848C ![]() 4849C ![]() 4850C ![]() 4851C ![]() 4852C ![]() 4853C ![]() 4854C ![]() 4855C ![]() 4856C ![]() 4857C ![]() 6rd4C ![]() 6rd5C ![]() 6rd6C ![]() 6rd7C ![]() 6rd8C ![]() 6rd9C ![]() 6rdaC ![]() 6rdbC ![]() 6rdcC ![]() 6rddC ![]() 6rdeC ![]() 6rdfC ![]() 6rdgC ![]() 6rdhC ![]() 6rdjC ![]() 6rdkC ![]() 6rdlC ![]() 6rdmC ![]() 6rdnC ![]() 6rdoC ![]() 6rdpC ![]() 6rdqC ![]() 6rdrC ![]() 6rdsC ![]() 6rdtC ![]() 6rduC ![]() 6rdvC ![]() 6rdwC ![]() 6rdxC ![]() 6rdyC ![]() 6rdzC ![]() 6re0C ![]() 6re1C ![]() 6re2C ![]() 6re3C ![]() 6re4C ![]() 6re5C ![]() 6re6C ![]() 6re7C ![]() 6re8C ![]() 6re9C ![]() 6reaC ![]() 6rebC ![]() 6recC ![]() 6redC ![]() 6reeC ![]() 6refC ![]() 6repC ![]() 6rerC ![]() 6resC ![]() 6retC ![]() 6reuC M: map data used to model this data C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 43.8 TB Data #1: Unaligned frames, gain reference corrected [micrographs - multiframe]) |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 4 types, 4 molecules 029Q
#1: Protein | Mass: 8731.866 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#3: Protein | Mass: 44842.121 Da / Num. of mol.: 1 / Mutation: P165F, N167S / Source method: isolated from a natural source / Source: (natural) ![]() |
#10: Protein | Mass: 11001.712 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#14: Protein | Mass: 8205.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-ATP synthase ... , 4 types, 8 molecules 1STUVXYZ
#2: Protein | Mass: 68679.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
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#16: Protein | Mass: 34639.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
#17: Protein | Mass: 60766.152 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() #18: Protein | Mass: 61939.070 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: A0ZW41, H+-transporting two-sector ATPase |
-Mitochondrial F1F0 ATP synthase associated ... , 2 types, 2 molecules 35
#4: Protein | Mass: 34850.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#6: Protein | Mass: 14004.376 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Mitochondrial ATP synthase associated protein ... , 2 types, 2 molecules 47
#5: Protein | Mass: 31275.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#8: Protein | Mass: 20553.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Mitochondrial ATP synthase subunit ... , 6 types, 15 molecules 68ABCDEFGHIJMPR
#7: Protein | Mass: 15904.290 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||
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#9: Protein | Mass: 9883.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||
#11: Protein | Mass: 12664.013 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) ![]() #12: Protein | | Mass: 34802.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #13: Protein | | Mass: 25530.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #15: Protein | | Mass: 20880.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 4 types, 11 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
#19: Chemical | ChemComp-ZN / | ||||
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#20: Chemical | #21: Chemical | ChemComp-MG / #22: Chemical | |
-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 F-ATP synthase dimer from Polytomella sp. Pringsheim 198.80 Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL |
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Molecular weight | Value: 1.6 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.8 |
Specimen | Conc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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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: 75000 X / Nominal defocus max: -5000 nm / Nominal defocus min: -400 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 35 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
Image scans | Width: 3840 / Height: 3712 |
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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: 735197 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124537 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL |