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- PDB-7tki: Yeast ATP synthase State 2catalytic(c) with 10 mM ATP backbone model -
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Open data
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Basic information
Entry | Database: PDB / ID: 7tki | ||||||||||||
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Title | Yeast ATP synthase State 2catalytic(c) with 10 mM ATP backbone model | ||||||||||||
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Function / homology | ![]() cristae formation / mitochondrial proton-transporting ATP synthase, central stalk / Formation of ATP by chemiosmotic coupling / Cristae formation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | 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 | ![]() | 601.2 KB | Display | ![]() |
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PDB format | ![]() | 371.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 25970MC ![]() 7tjsC ![]() 7tjtC ![]() 7tjuC ![]() 7tjvC ![]() 7tjwC ![]() 7tjxC ![]() 7tjyC ![]() 7tjzC ![]() 7tk0C ![]() 7tk1C ![]() 7tk2C ![]() 7tk3C ![]() 7tk4C ![]() 7tk5C ![]() 7tk6C ![]() 7tk7C ![]() 7tk8C ![]() 7tk9C ![]() 7tkaC ![]() 7tkbC ![]() 7tkcC ![]() 7tkdC ![]() 7tkeC ![]() 7tkfC ![]() 7tkgC ![]() 7tkhC ![]() 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 ... , 13 types, 26 molecules 0123456789ABCDEFGHIOTUVWXY
#1: Protein | ![]() Mass: 7762.375 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #2: Protein | ![]() Mass: 55007.402 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #3: Protein | ![]() Mass: 51181.082 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() References: UniProt: P00830, ![]() #4: Protein | | ![]() Mass: 30657.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #5: Protein | | ![]() Mass: 14565.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #6: Protein | | ![]() Mass: 6618.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #7: Protein | | ![]() Mass: 20901.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #8: Protein | | ![]() Mass: 27900.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #9: Protein | | ![]() Mass: 23194.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #10: Protein | | ![]() Mass: 19709.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #11: Protein | | ![]() Mass: 10584.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #12: Protein | | ![]() Mass: 10417.298 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #13: Protein | | ![]() Mass: 6696.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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-Protein/peptide , 1 types, 1 molecules Z
#14: Protein/peptide | ![]() Mass: 5825.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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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: Yeast ATP synthase State 2catalytic(c) with 10 mM ATP backbone model Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 0.61 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![]() ![]() |
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![]() ![]() |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 11.9 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 10037 |
Image scans | Width: 4096 / Height: 4096 |
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Processing
Software | Name: UCSF ChimeraX / Version: 1.2/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package | ||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2534488 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4213 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / 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 |