[English] 日本語
Yorodumi- EMDB-1640: Structure of the V-ATPase of Saccharomyces cerevisiae at 2.5 nm r... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1640 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the V-ATPase of Saccharomyces cerevisiae at 2.5 nm resolution | |||||||||
Map data | V-ATPase of Sacharomyces cerevisiae | |||||||||
Sample |
| |||||||||
Keywords | V-ATPase / single particle / Stator | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 25.0 Å | |||||||||
Authors | Diepholz M / Venzke D / Prinz S / Batisse C / Florchinger B / Rossle M / Svergun D / Bottcher B / Fethiere J | |||||||||
Citation | Journal: Structure / Year: 2008 Title: A different conformation for EGC stator subcomplex in solution and in the assembled yeast V-ATPase: possible implications for regulatory disassembly. Authors: Meikel Diepholz / David Venzke / Simone Prinz / Claire Batisse / Beate Flörchinger / Manfred Rössle / Dmitri I Svergun / Bettina Böttcher / James Féthière / Abstract: Vacuolar ATPases (V-ATPases) are ATP-dependent proton pumps that maintain the acidity of cellular compartments. They are composed of a membrane-integrated proton-translocating V(0) and an extrinsic ...Vacuolar ATPases (V-ATPases) are ATP-dependent proton pumps that maintain the acidity of cellular compartments. They are composed of a membrane-integrated proton-translocating V(0) and an extrinsic cytoplasmic catalytic domain V(1), joined by several connecting subunits. To clarify the arrangement of these peripheral connections and their interrelation with other subunits of the holocomplex, we have determined the solution structures of isolated EG and EGC connecting subcomplexes by small angle X-ray scattering and the 3D map of the yeast V-ATPase by electron microscopy. In solution, EG forms a slightly kinked rod, which assembles with subunit C into an L-shaped structure. This model is supported by the microscopy data, which show three copies of EG with two of these linked by subunit C. However, the relative arrangement of the EG and C subunits in solution is more open than that in the holoenzyme, suggesting a conformational change of EGC during regulatory assembly and disassembly. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1640.map.gz | 271.6 KB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-1640-v30.xml emd-1640.xml | 9.7 KB 9.7 KB | Display Display | EMDB header |
Images | vatpase_emdb.tif | 137.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1640 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1640 | HTTPS FTP |
-Validation report
Summary document | emd_1640_validation.pdf.gz | 198.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_1640_full_validation.pdf.gz | 197.4 KB | Display | |
Data in XML | emd_1640_validation.xml.gz | 5.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1640 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1640 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_1640.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | V-ATPase of Sacharomyces cerevisiae | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : V-ATPase
Entire | Name: V-ATPase |
---|---|
Components |
|
-Supramolecule #1000: V-ATPase
Supramolecule | Name: V-ATPase / type: sample / ID: 1000 / Oligomeric state: A3B3CDE3FG3Hac'c''c(5-8)d / Number unique components: 1 |
---|---|
Molecular weight | Theoretical: 980 KDa |
-Macromolecule #1: V-ATPase
Macromolecule | Name: V-ATPase / type: protein_or_peptide / ID: 1 / Name.synonym: V-ATPase / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast / Tissue: Inner membranes / Cell: SBY119 / Organelle: Vacuoles / Location in cell: Vacuolar membranes |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Experimental details
-Structure determination
Method | negative staining |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.1 Details: Phosphate buffered Saline containing 0.1% Digitonin, 8% sucrose, 2% sorbitol, 2% glucose, Pefabloc SC (Roche), 13 tablets/l of complete EDTA-free Protease inhibitors |
---|---|
Staining | Type: NEGATIVE Details: The sandwich technique (Golas et al., 2003) was used to prepare negatively stained V-ATPase samples. Briefly, purified V-ATPase at a concentration of 0.03 mg/ml was adsorbed on a carbon film ...Details: The sandwich technique (Golas et al., 2003) was used to prepare negatively stained V-ATPase samples. Briefly, purified V-ATPase at a concentration of 0.03 mg/ml was adsorbed on a carbon film layered on a mica support at the carbon/mica interface. Subsequently, the carbon film with adsorbed particles was floated over the staining solution (2% uranyl acetate). After attachment of a copper grid to the dry surface of the carbon, a second carbon film was floated over the same staining solution. The protein/carbon/grid assembly was picked up with a piece of newspaper, turned upside down, and immersed in the solution. A sandwich of two carbon layers with the protein particles trapped in between is created by picking up the second carbon layer with the grid. |
Grid | Details: 400 mesh copper grid |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
---|---|
Alignment procedure | Legacy - Astigmatism: Corrected at 200000 times magnification on graininess of carbon |
Image recording | Category: CCD / Film or detector model: GENERIC CCD / Digitization - Sampling interval: 14.22 µm / Number real images: 400 Details: Images were recorded on CCD, no scanning, sampling step size was adjusted to calibrated image size Bits/pixel: 12 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal magnification: 27500 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: SIDE ENTRY, EUCENTRIC |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC, SPIDER, EMAN Details: Spider option BP 32F Back Projection - 3D, Sampled, Interpolated in Fourier space Number images used: 16300 |
---|