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Open data
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Basic information
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Title | V/A-ATPase ftom Thermus thermophilus, high ATP, state1-2 | |||||||||||||||||||||
![]() | holo enzyme, state1-2 | |||||||||||||||||||||
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Biological species | ![]() ![]() | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||||||||
![]() | Kishikawa J / Nakanishi A / Nakano A / Saeki S / Furuta A / Kato T / Mitsuoka K / Yokoyama K | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural snapshots of V/A-ATPase reveal the rotary catalytic mechanism of rotary ATPases. Authors: J Kishikawa / A Nakanishi / A Nakano / S Saeki / A Furuta / T Kato / K Mistuoka / K Yokoyama / ![]() Abstract: V/A-ATPase is a motor protein that shares a common rotary catalytic mechanism with FF ATP synthase. When powered by ATP hydrolysis, the V domain rotates the central rotor against the AB hexamer, ...V/A-ATPase is a motor protein that shares a common rotary catalytic mechanism with FF ATP synthase. When powered by ATP hydrolysis, the V domain rotates the central rotor against the AB hexamer, composed of three catalytic AB dimers adopting different conformations (AB, AB, and AB). Here, we report the atomic models of 18 catalytic intermediates of the V domain of V/A-ATPase under different reaction conditions, determined by single particle cryo-EM. The models reveal that the rotor does not rotate immediately after binding of ATP to the V. Instead, three events proceed simultaneously with the 120˚ rotation of the shaft: hydrolysis of ATP in AB, zipper movement in AB by the binding ATP, and unzipper movement in AB with release of both ADP and Pi. This indicates the unidirectional rotation of V/A-ATPase by a ratchet-like mechanism owing to ATP hydrolysis in AB, rather than the power stroke model proposed previously for F-ATPase. | |||||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 304.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.4 KB 24.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 15.7 KB | Display | ![]() |
Images | ![]() | 139.1 KB | ||
Masks | ![]() | 325 MB | ![]() | |
Others | ![]() ![]() | 260 MB 260.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vaiC ![]() 7vajC ![]() 7vakC ![]() 7valC ![]() 7vamC ![]() 7vanC ![]() 7vaoC ![]() 7vapC ![]() 7vaqC ![]() 7varC ![]() 7vasC ![]() 7vatC ![]() 7vauC ![]() 7vavC ![]() 7vawC ![]() 7vaxC ![]() 7vayC ![]() 7vb0C C: citing same article ( |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | holo enzyme, state1-2 | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.88 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: holo enzyme, state1-1, half map A
File | emd_31848_half_map_1.map | ||||||||||||
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Annotation | holo enzyme, state1-1, half map A | ||||||||||||
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Density Histograms |
-Half map: holo enzyme, state1-1, half map B
File | emd_31848_half_map_2.map | ||||||||||||
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Annotation | holo enzyme, state1-1, half map B | ||||||||||||
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Density Histograms |
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Sample components
+Entire : V/A-ATPase from Thermus thermophilus, high ATP, state1-2
+Supramolecule #1: V/A-ATPase from Thermus thermophilus, high ATP, state1-2
+Macromolecule #1: A subunit of V/A-ATPase from Thermus thermophilus
+Macromolecule #2: B subunit of V/A-ATPase from Thermus thermophilus
+Macromolecule #3: D subunit of V/A-ATPase from Thermus thermophilus
+Macromolecule #4: F subunit of V/A-ATPase from Thermus thermophilus
+Macromolecule #5: E subunit of V/A-ATPase from Thermus thermophilus
+Macromolecule #6: G subunit of V/A-ATPase from Thermus thermophilus
+Macromolecule #7: a subunit of V/A-ATPase from Thermus thermophilus
+Macromolecule #8: d subunit of V/A-ATPase from Thermus thermophilus
+Macromolecule #9: c subunit of V/A-ATPase from Thermus thermophilus
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 / Details: contains 6 mM ATP-Mg |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 5.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.042 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |