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- EMDB-25964: Yeast ATP synthase State 1catalytic(g) with 10 mM ATP backbone model -
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Open data
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Basic information
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Title | Yeast ATP synthase State 1catalytic(g) with 10 mM ATP backbone model | ||||||||||||
![]() | Unsharpened map. | ||||||||||||
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![]() | F1-ATPase / ATP Synthase / Hydrolase / Nanomotor / Complex | ||||||||||||
Function / homology | ![]() : / cristae formation / : / : / Mitochondrial protein degradation / mitochondrial proton-transporting ATP synthase complex assembly / : / : / : / : ...: / cristae formation / : / : / Mitochondrial protein degradation / mitochondrial proton-transporting ATP synthase complex assembly / : / : / : / : / mitochondrial nucleoid / : / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / proton motive force-driven mitochondrial ATP synthesis / mitochondrial intermembrane space / ADP binding / protein-containing complex assembly / mitochondrial inner membrane / lipid binding / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.8 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. #1: ![]() Title: Structure of ATP synthase under strain during catalysis Authors: Guo H / Rubinstein JL | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 32 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 32.3 KB 32.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.5 KB | Display | ![]() |
Images | ![]() | 50.7 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 8 KB | ||
Others | ![]() ![]() | 59.4 MB 59.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7tkcMC ![]() 7tjsC ![]() 7tjtC ![]() 7tjuC ![]() 7tjvC ![]() 7tjwC ![]() 7tjxC ![]() 7tjyC ![]() 7tjzC ![]() 7tk0C ![]() 7tk1C ![]() 7tk2C ![]() 7tk3C ![]() 7tk4C ![]() 7tk5C ![]() 7tk6C ![]() 7tk7C ![]() 7tk8C ![]() 7tk9C ![]() 7tkaC ![]() 7tkbC ![]() 7tkdC ![]() 7tkeC ![]() 7tkfC ![]() 7tkgC ![]() 7tkhC ![]() 7tkiC ![]() 7tkjC ![]() 7tkkC ![]() 7tklC ![]() 7tkmC ![]() 7tknC ![]() 7tkoC ![]() 7tkpC ![]() 7tkqC ![]() 7tkrC ![]() 7tksC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Unsharpened map. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.3475 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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Density Histograms |
-Half map: #2
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Density Histograms |
-Half map: #1
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Density Histograms |
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Sample components
+Entire : Yeast ATP synthase State 1catalytic(g) with 10 mM ATP backbone model
+Supramolecule #1: Yeast ATP synthase State 1catalytic(g) with 10 mM ATP backbone model
+Macromolecule #1: ATP synthase subunit 9, mitochondrial
+Macromolecule #2: ATP synthase subunit alpha
+Macromolecule #3: ATP synthase subunit beta
+Macromolecule #4: ATP synthase subunit gamma
+Macromolecule #5: ATP synthase subunit delta
+Macromolecule #6: ATP synthase subunit epsilon
+Macromolecule #7: ATP synthase subunit 5
+Macromolecule #8: ATP synthase subunit a
+Macromolecule #9: ATP synthase subunit 4
+Macromolecule #10: ATP synthase subunit d
+Macromolecule #11: ATP synthase subunit f
+Macromolecule #12: ATP synthase subunit H
+Macromolecule #13: ATP synthase subunit J
+Macromolecule #14: ATP synthase protein 8
-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: 10037 / Average exposure time: 11.9 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 103896 / 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: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |