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- PDB-7tjt: Yeast ATP synthase F1 region State 1-3catalytic beta_tight open w... -
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Basic information
Entry | Database: PDB / ID: 7tjt | ||||||||||||
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Title | Yeast ATP synthase F1 region State 1-3catalytic beta_tight open without exogenous ATP | ||||||||||||
![]() | (ATP synthase subunit ...) x 3 | ||||||||||||
![]() | HYDROLASE / F1-ATPase / ATP Synthase / Nanomotor / Complex | ||||||||||||
Function / homology | ![]() : / : / : / Mitochondrial protein degradation / : / : / mitochondrial nucleoid / : / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis ...: / : / : / Mitochondrial protein degradation / : / : / mitochondrial nucleoid / : / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / 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 / mitochondrial intermembrane space / ADP binding / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion / ATP binding / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
![]() | Guo, H. / Rubinstein, J.L. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of ATP synthase under strain during catalysis. Authors: Hui Guo / John L Rubinstein / ![]() Abstract: ATP synthases are macromolecular machines consisting of an ATP-hydrolysis-driven F motor and a proton-translocation-driven F motor. The F and F motors oppose each other's action on a shared rotor ...ATP synthases are macromolecular machines consisting of an ATP-hydrolysis-driven F motor and a proton-translocation-driven F motor. The F and F motors oppose each other's action on a shared rotor subcomplex and are held stationary relative to each other by a peripheral stalk. Structures of resting mitochondrial ATP synthases revealed a left-handed curvature of the peripheral stalk even though rotation of the rotor, driven by either ATP hydrolysis in F or proton translocation through F, would apply a right-handed bending force to the stalk. We used cryoEM to image yeast mitochondrial ATP synthase under strain during ATP-hydrolysis-driven rotary catalysis, revealing a large deformation of the peripheral stalk. The structures show how the peripheral stalk opposes the bending force and suggests that during ATP synthesis proton translocation causes accumulation of strain in the stalk, which relaxes by driving the relative rotation of the rotor through six sub-steps within F, leading to catalysis. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 506.7 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 25931MC ![]() 7tjsC ![]() 7tjuC ![]() 7tjvC ![]() 7tjwC ![]() 7tjxC ![]() 7tjyC ![]() 7tjzC ![]() 7tk0C ![]() 7tk1C ![]() 7tk2C ![]() 7tk3C ![]() 7tk4C ![]() 7tk5C ![]() 7tk6C ![]() 7tk7C ![]() 7tk8C ![]() 7tk9C ![]() 7tkaC ![]() 7tkbC ![]() 7tkcC ![]() 7tkdC ![]() 7tkeC ![]() 7tkfC ![]() 7tkgC ![]() 7tkhC ![]() 7tkiC ![]() 7tkjC ![]() 7tkkC ![]() 7tklC ![]() 7tkmC ![]() 7tknC ![]() 7tkoC ![]() 7tkpC ![]() 7tkqC ![]() 7tkrC ![]() 7tksC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-ATP synthase subunit ... , 3 types, 7 molecules ABCDEFG
#1: Protein | Mass: 55007.402 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 51181.082 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P00830, H+-transporting two-sector ATPase #3: Protein | | Mass: 30657.160 Da / Num. of mol.: 1 / 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/MG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PO4.gif)
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PO4 / | |
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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: Yeast ATP synthase F1 region State 1-3catalytic beta_tight open without exogenous ATP Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL |
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Molecular weight | Value: 0.4 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER/RHODIUM / Grid mesh size: 300 divisions/in. / Grid type: Homemade |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE-PROPANE / 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 / Calibrated magnification: 133843 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1100 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10.1 sec. / Electron dose: 39 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 8817 |
Image scans | Width: 4096 / Height: 4096 |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 442025 | ||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 144275 / Algorithm: BACK PROJECTION / Num. of class averages: 3 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: RECIPROCAL | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 2HLD Accession code: 2HLD / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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