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Open data
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Basic information
Entry | Database: PDB / ID: 6vog | ||||||
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Title | Chloroplast ATP synthase (O2, CF1) | ||||||
![]() | (ATP synthase ...) x 5 | ||||||
![]() | TRANSLOCASE / PHOTOSYNTHESIS / CF1FO / ATP synthase | ||||||
Function / homology | ![]() : / : / photosynthetic electron transport in photosystem I / : / proton motive force-driven ATP synthesis / chloroplast thylakoid membrane / 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 ...: / : / photosynthetic electron transport in photosystem I / : / proton motive force-driven ATP synthesis / chloroplast thylakoid membrane / 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 / proton motive force-driven mitochondrial ATP synthesis / ADP binding / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.35 Å | ||||||
![]() | Yang, J.-H. / Williams, D. / Kandiah, E. / Fromme, P. / Chiu, P.-L. | ||||||
![]() | ![]() Title: Structural basis of redox modulation on chloroplast ATP synthase. Authors: Jay-How Yang / Dewight Williams / Eaazhisai Kandiah / Petra Fromme / Po-Lin Chiu / ![]() ![]() Abstract: In higher plants, chloroplast ATP synthase has a unique redox switch on its γ subunit that modulates enzyme activity to limit ATP hydrolysis at night. To understand the molecular details of the ...In higher plants, chloroplast ATP synthase has a unique redox switch on its γ subunit that modulates enzyme activity to limit ATP hydrolysis at night. To understand the molecular details of the redox modulation, we used single-particle cryo-EM to determine the structures of spinach chloroplast ATP synthase in both reduced and oxidized states. The disulfide linkage of the oxidized γ subunit introduces a torsional constraint to stabilize the two β hairpin structures. Once reduced, free cysteines alleviate this constraint, resulting in a concerted motion of the enzyme complex and a smooth transition between rotary states to facilitate the ATP synthesis. We added an uncompetitive inhibitor, tentoxin, in the reduced sample to limit the flexibility of the enzyme and obtained high-resolution details. Our cryo-EM structures provide mechanistic insight into the redox modulation of the energy regulation activity of chloroplast ATP synthase. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 594.9 KB | Display | ![]() |
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PDB format | ![]() | 497.7 KB | 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 | ![]() 21263MC ![]() 6vm1C ![]() 6vm4C ![]() 6vmbC ![]() 6vmdC ![]() 6vmgC ![]() 6vofC ![]() 6vohC ![]() 6voiC ![]() 6vojC ![]() 6vokC ![]() 6volC ![]() 6vomC ![]() 6vonC ![]() 6vooC 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
-ATP synthase ... , 5 types, 9 molecules ABCDEFdge
#1: Protein | Mass: 55505.199 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P06450, H+-transporting two-sector ATPase #2: Protein | Mass: 53797.367 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P00825, H+-transporting two-sector ATPase #3: Protein | | Mass: 27708.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | | Mass: 40119.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | | Mass: 14715.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 2 types, 5 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/ADP.gif)
#6: Chemical | ChemComp-ATP / #7: 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: Chloroplast ATP synthase / Type: COMPLEX / Details: Oxidized rotary state 2 (CF1) / Entity ID: #1-#5 / Source: NATURAL |
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Molecular weight | Value: 0.59435 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: C-flat-1.2/1.3 4C |
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: 22500 X / Calibrated magnification: 48077 X / Nominal defocus max: -4000 nm / Nominal defocus min: -1500 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: 43.5 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 114542 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6FKH | ||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 158.36 Å2 | ||||||||||||||||||||||||||||||||||||
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