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- EMDB-1888: Thermus thermophilus V-type (A-type) ATPase at 16 Angstroms resolution -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1888 | |||||||||
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Title | Thermus thermophilus V-type (A-type) ATPase at 16 Angstroms resolution | |||||||||
![]() | Thermus thermophilus V-type (A-type) ATPase | |||||||||
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![]() | Vacuolar type ATPase / V-ATPase / A-ATPase / Thermus thermophilus / ATP synthase / membrane protein | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 16.0 Å | |||||||||
![]() | Lau WCY / Rubinstein JL | |||||||||
![]() | ![]() Title: Structure of intact Thermus thermophilus V-ATPase by cryo-EM reveals organization of the membrane-bound V(O) motor. Authors: Wilson C Y Lau / John L Rubinstein / ![]() Abstract: The eubacterium Thermus thermophilus uses a macromolecular assembly closely related to eukaryotic V-ATPase to produce its supply of ATP. This simplified V-ATPase offers several advantages over ...The eubacterium Thermus thermophilus uses a macromolecular assembly closely related to eukaryotic V-ATPase to produce its supply of ATP. This simplified V-ATPase offers several advantages over eukaryotic V-ATPases for structural analysis and investigation of the mechanism of the enzyme. Here we report the structure of the complex at approximately 16 A resolution as determined by single particle electron cryomicroscopy (cryo-EM). The resolution of the map and our use of cryo-EM, rather than negative stain EM, reveals detailed information about the internal organization of the assembly. We could separate the map into segments corresponding to subunits A and B, the threefold pseudosymmetric C-subunit, a central rotor consisting of subunits D and F, the L-ring, the stator subcomplex consisting of subunits I, E, and G, and a micelle of bound detergent. The architecture of the V(O) region shows a remarkably small area of contact between the I-subunit and the ring of L-subunits and is consistent with a two half-channel model for proton translocation. The arrangement of structural elements in V(O) gives insight into the mechanism of torque generation from proton translocation. | |||||||||
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 | ![]() | 7.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 8.2 KB 8.2 KB | Display Display | ![]() |
Images | ![]() | 91.3 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 904 B 7.4 MB 7.4 MB 7.4 MB 7.4 MB 7.4 MB 7.4 MB 7.4 MB 7.4 MB 7.4 MB 7.4 MB 7.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 214.5 KB | Display | ![]() |
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Full document | ![]() | 213.7 KB | Display | |
Data in XML | ![]() | 5.6 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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Annotation | Thermus thermophilus V-type (A-type) ATPase | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
+Supplemental map: emd 1888 additional 1.map
+Supplemental map: emd 1888 additional 10.map
+Supplemental map: emd 1888 additional 11.map
+Supplemental map: emd 1888 additional 2.map
+Supplemental map: emd 1888 additional 3.map
+Supplemental map: emd 1888 additional 4.map
+Supplemental map: emd 1888 additional 5.map
+Supplemental map: emd 1888 additional 6.map
+Supplemental map: emd 1888 additional 7.map
+Supplemental map: emd 1888 additional 8.map
+Supplemental map: emd 1888 additional 9.map
+Others
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Sample components
-Entire : V/A-ATPase from Thermus thermophilus solubilized with the deterge...
Entire | Name: V/A-ATPase from Thermus thermophilus solubilized with the detergent dodecyl maltoside. |
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Components |
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-Supramolecule #1000: V/A-ATPase from Thermus thermophilus solubilized with the deterge...
Supramolecule | Name: V/A-ATPase from Thermus thermophilus solubilized with the detergent dodecyl maltoside. type: sample / ID: 1000 / Oligomeric state: Hetero 26mer / Number unique components: 9 |
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Molecular weight | Theoretical: 600 KDa |
-Supramolecule #1: V-ATPase
Supramolecule | Name: V-ATPase / type: organelle_or_cellular_component / ID: 1 / Name.synonym: ATPase / Recombinant expression: No |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2.0 mg/mL |
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Buffer | pH: 8 / Details: 50mM Tris-HCl 150mM NaCL 5mM MgCl2 O.02% DDM |
Grid | Details: Quantifoil 2/2 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III / Details: Vitrification instrument: Vitrobot Mark III / Method: Blot approx. 20 seconds. |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7.0 µm / Average electron dose: 25 e/Å2 / Details: Images averaged 2x2 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Gatan 626 / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
Details | Particle images were manually selected with Ximdisp. |
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CTF correction | Details: MRC |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: OTHER / Software - Name: Rotan, Frealign / Number images used: 19825 |