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- EMDB-4700: Thermus thermophilus V/A-type ATPase/synthase, rotational state 3 -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4700 | |||||||||
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Title | Thermus thermophilus V/A-type ATPase/synthase, rotational state 3 | |||||||||
![]() | A combined map from focused refinements of several domains of the intact complex as described in the paper. | |||||||||
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![]() | ATP hydrolysis/synthesis / proton translocation / rotary catalysis / MEMBRANE 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: 3.9 Å | |||||||||
![]() | Zhou L / Sazanov L | |||||||||
![]() | ![]() Title: Structure and conformational plasticity of the intact V/A-type ATPase. Authors: Long Zhou / Leonid A Sazanov / ![]() Abstract: V (vacuolar)/A (archaeal)-type adenosine triphosphatases (ATPases), found in archaea and eubacteria, couple ATP hydrolysis or synthesis to proton translocation across the plasma membrane using the ...V (vacuolar)/A (archaeal)-type adenosine triphosphatases (ATPases), found in archaea and eubacteria, couple ATP hydrolysis or synthesis to proton translocation across the plasma membrane using the rotary-catalysis mechanism. They belong to the V-type ATPase family, which differs from the mitochondrial/chloroplast F-type ATP synthases in overall architecture. We solved cryo-electron microscopy structures of the intact V/A-ATPase, reconstituted into lipid nanodiscs, in three rotational states and two substates. These structures indicate substantial flexibility between V and V in a working enzyme, which results from mechanical competition between central shaft rotation and resistance from the peripheral stalks. We also describe details of adenosine diphosphate inhibition release, V-V torque transmission, and proton translocation, which are relevant for the entire V-type ATPase family. | |||||||||
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 | ![]() | 3.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 35.3 KB 35.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17 KB | Display | ![]() |
Images | ![]() | 164.7 KB | ||
Filedesc metadata | ![]() | 8.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6r0yMC ![]() 4640C ![]() 4699C ![]() 4702C ![]() 4703C ![]() 6qumC ![]() 6r0wC ![]() 6r0zC ![]() 6r10C C: citing same article ( M: atomic model generated by this map |
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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
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | A combined map from focused refinements of several domains of the intact complex as described in the paper. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.085 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 : Thermus thermophilus V/A-type ATPase/ATP synthase
+Supramolecule #1: Thermus thermophilus V/A-type ATPase/ATP synthase
+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: MAGNESIUM ION
+Macromolecule #11: 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 | 5.4 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 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: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 2700 / Average exposure time: 63.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated defocus max: 1.78 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 129032 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 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 |
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Refinement | Space: REAL / Overall B value: 112.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Output model | ![]() PDB-6r0y: |