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Open data
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Basic information
Entry | Database: PDB / ID: 5t4q | ||||||
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Title | Autoinhibited E. coli ATP synthase state 3 | ||||||
![]() | (ATP synthase ...) x 8 | ||||||
![]() | HYDROLASE / ATP synthase / ATPase / rotary motor / membrane protein | ||||||
Function / homology | ![]() proton-transporting ATP synthase complex / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / photosynthetic electron transport in photosystem I / proton-transporting ATP synthase complex, catalytic core F(1) / photosynthetic electron transport in photosystem II / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism ...proton-transporting ATP synthase complex / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / photosynthetic electron transport in photosystem I / proton-transporting ATP synthase complex, catalytic core F(1) / photosynthetic electron transport in photosystem II / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / lipid binding / ATP hydrolysis activity / ATP binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.53 Å | ||||||
![]() | Sobti, M. / Smits, C. / Wong, A.S.W. / Ishmukhametov, R. / Stock, D. / Sandin, S. / Stewart, A.G. | ||||||
![]() | ![]() Title: Cryo-EM structures of the autoinhibited ATP synthase in three rotational states. Authors: Meghna Sobti / Callum Smits / Andrew Sw Wong / Robert Ishmukhametov / Daniela Stock / Sara Sandin / Alastair G Stewart / ![]() ![]() ![]() Abstract: A molecular model that provides a framework for interpreting the wealth of functional information obtained on the F-ATP synthase has been generated using cryo-electron microscopy. Three different ...A molecular model that provides a framework for interpreting the wealth of functional information obtained on the F-ATP synthase has been generated using cryo-electron microscopy. Three different states that relate to rotation of the enzyme were observed, with the central stalk's ε subunit in an extended autoinhibitory conformation in all three states. The F motor comprises of seven transmembrane helices and a decameric c-ring and invaginations on either side of the membrane indicate the entry and exit channels for protons. The proton translocating subunit contains near parallel helices inclined by ~30° to the membrane, a feature now synonymous with rotary ATPases. For the first time in this rotary ATPase subtype, the peripheral stalk is resolved over its entire length of the complex, revealing the F attachment points and a coiled-coil that bifurcates toward the membrane with its helices separating to embrace subunit from two sides. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 680.6 KB | Display | ![]() |
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PDB format | ![]() | 479.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 98.4 KB | Display | |
Data in CIF | ![]() | 164.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8359MC ![]() 8357C ![]() 8358C ![]() 5t4oC ![]() 5t4pC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
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Components
-ATP synthase ... , 8 types, 22 molecules ABCDEFGHIJKLMNOPQRSTUV
#1: Protein | Mass: 55138.531 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: B7MGF4, UniProt: P0ABB0*PLUS, H+-transporting two-sector ATPase #2: Protein | Mass: 51664.574 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: B7MGF2, UniProt: P0ABB4*PLUS, H+-transporting two-sector ATPase #3: Protein | | Mass: 31539.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Protein | | Mass: 15087.244 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #5: Protein | Mass: 17126.691 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #6: Protein | | Mass: 30324.096 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #7: Protein | | Mass: 19289.061 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #8: Protein | Mass: 8259.064 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 2 types, 4 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/ADP.gif)
#9: Chemical | #10: Chemical | ChemComp-ADP / | |
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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: ATP synthase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.558 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | 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 |
Image recording | Electron dose: 29 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 8.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 95345 / Symmetry type: POINT |