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- EMDB-3546: Structure of a novel N-type ATPase rotor ring (c17) from Burkhold... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3546 | |||||||||
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Title | Structure of a novel N-type ATPase rotor ring (c17) from Burkholderia pseudomallei | |||||||||
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Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.1 Å | |||||||||
![]() | Wilkes M / Schulz S / Mills DJ / Kuhlbrandt W / Meier T | |||||||||
![]() | ![]() Title: Molecular architecture of the N-type ATPase rotor ring from . Authors: Sarah Schulz / Martin Wilkes / Deryck J Mills / Werner Kühlbrandt / Thomas Meier / ![]() Abstract: The genome of the highly infectious bacterium harbors an operon that encodes an N-type rotary ATPase, in addition to an operon for a regular F-type rotary ATPase. The molecular architecture of N- ...The genome of the highly infectious bacterium harbors an operon that encodes an N-type rotary ATPase, in addition to an operon for a regular F-type rotary ATPase. The molecular architecture of N-type ATPases is unknown and their biochemical properties and cellular functions are largely unexplored. We studied the NN-type ATPase and investigated the structure and ion specificity of its membrane-embedded c-ring rotor by single-particle electron cryo-microscopy. Of several amphiphilic compounds tested for solubilizing the complex, the choice of the low-density, low-CMC detergent LDAO was optimal in terms of map quality and resolution. The cryoEM map of the c-ring at 6.1 Å resolution reveals a heptadecameric oligomer with a molecular mass of ~141 kDa. Biochemical measurements indicate that the c ring is H specific, demonstrating that the ATPase is proton-coupled. The c ring stoichiometry results in a very high ion-to-ATP ratio of 5.7. We propose that this N-ATPase is a highly efficient proton pump that helps these melioidosis-causing bacteria to survive in the hostile, acidic environment of phagosomes. | |||||||||
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 | ![]() | 7.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 8.5 KB 8.5 KB | Display Display | ![]() |
Images | ![]() | 42.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 232.7 KB | Display | ![]() |
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Full document | ![]() | 231.9 KB | Display | |
Data in XML | ![]() | 5.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.14 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 : Rotor ring of the N-type ATPase from B. pseudomallei
Entire | Name: Rotor ring of the N-type ATPase from B. pseudomallei |
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Components |
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-Supramolecule #1: Rotor ring of the N-type ATPase from B. pseudomallei
Supramolecule | Name: Rotor ring of the N-type ATPase from B. pseudomallei / type: complex / ID: 1 / Parent: 0 Details: We determined the molecular architecture of the N-type ATPase rotor ring in the melioidosis-causing bacterium Burkholderia pseudomallei by electron cryo-microscopy. The structure shows an ...Details: We determined the molecular architecture of the N-type ATPase rotor ring in the melioidosis-causing bacterium Burkholderia pseudomallei by electron cryo-microscopy. The structure shows an unusually large c-ring rotor with 17 subunits that, in the acidic environment of the host phagosome, is driven predominantly by protons. |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Experimental: 8.3 kDa/nm |
-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: 7.5 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK III |
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Electron microscopy
Microscope | JEOL 3200FSC |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm |
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Image processing
Final reconstruction | Applied symmetry - Point group: C17 (17 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47000 |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |