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- EMDB-6813: V/A-type ATPase/synthase from Thermus thermophilus, rotational st... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6813 | |||||||||
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Title | V/A-type ATPase/synthase from Thermus thermophilus, rotational state 3. | |||||||||
![]() | V/A-type ATPase/synthase from Thermus thermophilus, rotational state 3. | |||||||||
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![]() | ATP synthase / proton pump / V-ATPase / Bioenergetics / MOTOR PROTEIN | |||||||||
Function / homology | ![]() proton-transporting V-type ATPase, V0 domain / 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 V-type ATPase, V0 domain / 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 / ATPase binding / lysosomal membrane / ATP binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.5 Å | |||||||||
![]() | Nakanishi A / Kishikawa J | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo EM structure of intact rotary H-ATPase/synthase from Thermus thermophilus. Authors: Atsuko Nakanishi / Jun-Ichi Kishikawa / Masatada Tamakoshi / Kaoru Mitsuoka / Ken Yokoyama / ![]() Abstract: Proton translocating rotary ATPases couple ATP hydrolysis/synthesis, which occurs in the soluble domain, with proton flow through the membrane domain via a rotation of the common central rotor ...Proton translocating rotary ATPases couple ATP hydrolysis/synthesis, which occurs in the soluble domain, with proton flow through the membrane domain via a rotation of the common central rotor complex against the surrounding peripheral stator apparatus. Here, we present a large data set of single particle cryo-electron micrograph images of the V/A type H-rotary ATPase from the bacterium Thermus thermophilus, enabling the identification of three rotational states based on the orientation of the rotor subunit. Using masked refinement and classification with signal subtractions, we obtain homogeneous reconstructions for the whole complexes and soluble V domains. These reconstructions are of higher resolution than any EM map of intact rotary ATPase reported previously, providing a detailed molecular basis for how the rotary ATPase maintains structural integrity of the peripheral stator apparatus, and confirming the existence of a clear proton translocation path from both sides of the membrane. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 46.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.4 KB 22.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.9 KB | Display | ![]() |
Images | ![]() | 54 KB | ||
Filedesc metadata | ![]() | 7.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5y60MC ![]() 6810C ![]() 6811C ![]() 6812C ![]() 5y5xC ![]() 5y5yC ![]() 5y5zC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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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 | V/A-type ATPase/synthase from Thermus thermophilus, rotational state 3. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : V/A-type ATPase/synthase from Thermus thermophilus, rotational st...
+Supramolecule #1: V/A-type ATPase/synthase from Thermus thermophilus, rotational st...
+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 (VAPC-THERM)
+Macromolecule #6: V-type ATP synthase subunit E
+Macromolecule #7: V-type ATP synthase subunit C
+Macromolecule #8: V-type ATP synthase subunit I
+Macromolecule #9: V-type ATP synthase, subunit K
+Macromolecule #10: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.027 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/2 / Material: MOLYBDENUM / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 1.0 sec. / Average electron dose: 26.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |