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- EMDB-25943: Yeast ATP synthase F1 region State 3catalytic beta_tight open wit... -
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Open data
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Basic information
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Title | Yeast ATP synthase F1 region State 3catalytic beta_tight open without exogenous ATP | ||||||||||||
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![]() | F1-ATPase / ATP Synthase / Hydrolase / Nanomotor / Complex | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||
![]() | Guo H / Rubinstein JL | ||||||||||||
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. | ||||||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.3 KB 18.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.8 KB | Display | ![]() |
Images | ![]() | 80.4 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 4.5 KB | ||
Others | ![]() ![]() ![]() | 32.3 MB 59.5 MB 59.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 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 ![]() 7tkiC ![]() 7tkjC ![]() 7tkkC ![]() 7tklC ![]() 7tkmC ![]() 7tknC ![]() 7tkoC ![]() 7tkpC ![]() 7tkqC ![]() 7tkrC ![]() 7tksC C: citing same article ( |
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Links
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Map
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Voxel size | X=Y=Z: 1.3075 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Additional map: Unsharpened map.
File | emd_25943_additional_1.map | ||||||||||||
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Annotation | Unsharpened map. | ||||||||||||
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Density Histograms |
-Half map: #1
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Density Histograms |
-Half map: #2
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Density Histograms |
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Sample components
-Entire : Yeast ATP synthase F1 region State 3catalytic beta_tight open wit...
Entire | Name: Yeast ATP synthase F1 region State 3catalytic beta_tight open without exogenous ATP |
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Components |
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-Supramolecule #1: Yeast ATP synthase F1 region State 3catalytic beta_tight open wit...
Supramolecule | Name: Yeast ATP synthase F1 region State 3catalytic beta_tight open without exogenous ATP type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 400 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 15 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Homemade / Material: COPPER/RHODIUM / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 35 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: LEICA EM GP |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 8817 / Average exposure time: 10.1 sec. / Average electron dose: 39.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 133843 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: RECIPROCAL / Protocol: RIGID BODY FIT |