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Open data
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Basic information
Entry | Database: PDB / ID: 6vol | ||||||
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Title | Chloroplast ATP synthase (R2, CF1FO) | ||||||
![]() | (ATP synthase ...![]() | ||||||
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Function / homology | ![]() proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton motive force-driven mitochondrial ATP synthesis / chloroplast thylakoid membrane / proton-transporting ATP synthase complex, catalytic core F(1) / ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 852.4 KB | Display | ![]() |
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PDB format | ![]() | 695.6 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 | ![]() 21268MC ![]() 6vm1C ![]() 6vm4C ![]() 6vmbC ![]() 6vmdC ![]() 6vmgC ![]() 6vofC ![]() 6vogC ![]() 6vohC ![]() 6voiC ![]() 6vojC ![]() 6vokC ![]() 6vomC ![]() 6vonC ![]() 6vooC M: map data used to model this data C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 109.9 Data #1: Reduced state of the chloroplast ATP synthase [micrographs - single frame]) |
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Links
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Assembly
Deposited unit | ![]()
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Components
-ATP synthase ... , 9 types, 26 molecules ABCDEFdgeIJaMNOPQRSTUVWXYZ
#1: Protein | ![]() Mass: 55505.199 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P06450, ![]() #2: Protein | ![]() Mass: 53797.367 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P00825, ![]() #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) ![]() ![]() #6: Protein | | ![]() Mass: 21013.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | | ![]() Mass: 24487.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | | ![]() Mass: 27102.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | ![]() Mass: 7977.366 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 3 types, 7 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/TTX.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/TTX.gif)
#10: Chemical | ChemComp-ATP / ![]() #11: Chemical | ![]() #12: Chemical | ChemComp-TTX / | ![]() |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Chloroplast ATP synthase / Type: COMPLEX / Details: Reduced rotary state 2 (CF1FO) / Entity ID: #1-#9 / 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![]() ![]() |
Specimen support | Grid material: COPPER / Grid type: C-flat-2/2 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![]() ![]() |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 43.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter name![]() |
Image scans | Sampling size: 5 µm |
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Processing
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() | ||||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 4.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29667 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6FKH Accession code: 6FKH / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.93 Å2 | ||||||||||||||||||||||||||||||||||||
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