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- EMDB-31861: V1EG domain of V/A-ATPase from Thermus thermophilus at low ATP co... -
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Basic information
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Title | V1EG domain of V/A-ATPase from Thermus thermophilus at low ATP concentration, state1-2 | |||||||||||||||||||||
![]() | V1EG domain of V/A-ATPase from Thermus thermophilus at low ATP concentration, state1-2, postprocessed map. | |||||||||||||||||||||
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![]() | rotary ATPase / V-type ATPase / ATP synthase / Thermus thermophilus / chemo-mechanical coupling / MOTOR PROTEIN | |||||||||||||||||||||
Function / homology | ![]() proton-transporting two-sector ATPase complex, catalytic domain / vacuolar proton-transporting V-type ATPase complex / proton-transporting ATP synthase complex / plant-type vacuole / vacuolar acidification / proton motive force-driven plasma membrane ATP synthesis / fungal-type vacuole membrane / H+-transporting two-sector ATPase / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism ...proton-transporting two-sector ATPase complex, catalytic domain / vacuolar proton-transporting V-type ATPase complex / proton-transporting ATP synthase complex / plant-type vacuole / vacuolar acidification / proton motive force-driven plasma membrane ATP synthesis / fungal-type vacuole membrane / H+-transporting two-sector ATPase / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / lysosomal membrane / ATP binding / metal ion binding Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 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 | ![]() | 228.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 25.2 KB 25.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.2 KB | Display | ![]() |
Images | ![]() | 58.2 KB | ||
Masks | ![]() | 244.1 MB | ![]() | |
Filedesc metadata | ![]() | 7 KB | ||
Others | ![]() ![]() | 194.8 MB 194.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vasMC ![]() 7vaiC ![]() 7vajC ![]() 7vakC ![]() 7valC ![]() 7vamC ![]() 7vanC ![]() 7vaoC ![]() 7vapC ![]() 7vaqC ![]() 7varC ![]() 7vatC ![]() 7vauC ![]() 7vavC ![]() 7vawC ![]() 7vaxC ![]() 7vayC ![]() 7vb0C 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 | V1EG domain of V/A-ATPase from Thermus thermophilus at low ATP concentration, state1-2, postprocessed map. | ||||||||||||||||||||
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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Projections & Slices |
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Density Histograms |
-Half map: V1EG domain of V/A-ATPase from Thermus thermophilus at...
File | emd_31861_half_map_1.map | ||||||||||||
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Annotation | V1EG domain of V/A-ATPase from Thermus thermophilus at low ATP concentration, state1-2, halfmap1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: V1EG domain of V/A-ATPase from Thermus thermophilus at...
File | emd_31861_half_map_2.map | ||||||||||||
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Annotation | V1EG domain of V/A-ATPase from Thermus thermophilus at low ATP concentration, state1-2, halfmap2. | ||||||||||||
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Density Histograms |
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Sample components
+Entire : V1EG domain of V/A-ATPase from Thermus thermophilus at low ATP co...
+Supramolecule #1: V1EG domain of V/A-ATPase from Thermus thermophilus at low ATP co...
+Macromolecule #1: V-type ATP synthase alpha chain
+Macromolecule #2: V-type ATP synthase beta chain
+Macromolecule #3: V-type ATP synthase subunit D
+Macromolecule #4: V-type ATP synthase subunit F
+Macromolecule #5: V-type ATP synthase subunit G
+Macromolecule #6: V-type ATP synthase subunit E
+Macromolecule #7: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #8: MAGNESIUM ION
+Macromolecule #9: ADENOSINE-5'-TRIPHOSPHATE
-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: Buffer contains 50 micromolar ATP. |
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Grid | Model: Quantifoil R1.2/1.3 / Material: MOLYBDENUM / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. |
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: 0.071 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 |
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Image processing
-Atomic model buiding 1
Details | The atomic model built in this study was used as an initial model. |
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Refinement | Space: REAL / Protocol: OTHER |
Output model | ![]() PDB-7vas: |