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Structure of the V-ATPase of Saccharomyces cerevisiae at 2.5 nm resolution
by single particle reconstruction, at 25 A resolution
#1: Surface view with section colored by density value, Surface level: 0.05, Made by UCSF CHIMERA
#2: Surface view colored by cylindrical radius, Surface level: 0.05, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1640 |
|---|---|
| Authors | Diepholz M, Venzke D, Prinz S, Batisse C, Florchinger B, Rossle M, Svergun D, Bottcher B, Fethiere J |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 0.05, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 0.05, Made by UCSF CHIMERA |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Map | |||||||||||||||||||||||||
| File |  EMD-1640.map ( map file in CCP4 format, 4002 KB ) | ||||||||||||||||||||||||
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| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A = 517 A , B = 517 A , C = 517 A , alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 5.17 A , Y = 5.17 A , Z = 5.17 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | V-ATPase of Sacharomyces cerevisiae | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | V-ATPase |
|---|---|
| Number of Components | 1 |
| Oligomeric State | A3B3CDE3FG3Hac'c''c(5-8)d |
| Theoretical Mass | 0.98 MDa |
| Component #1: protein - V-ATPase | |
| Scientific name | V-ATPase |
| Scientific Name of Species | Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
|
| Common Name of Species | Baker's Yeast |
| Recombinant expression | Yes |
| Natural Source | Cell: SBY119 Organ Or Tissue: Inner membranes Organelle: Vacuoles Cell Location: Vacuolar membranes |
| Engineered Source | Exp System: Saccharomyces cerevisiae (NCBI Taxonomy: 4932) |
 Experiment | |
| Sample Preparation | |
| Staining | 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. |
|---|---|
| Specimen Support Details | 400 mesh copper grid |
| Specimen State | particle |
| Buffer | 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 pH: 7.1 |
| Vitrification | |
| Cryogen Name | NONE |
| Instrument | NONE |
| Imaging | |
| Microscope | FEI/PHILIPS CM200FEG |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 27500 X, |
| Astigmatism | Corrected at 200000 times magnification on graininess of carbon |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder | |
| Holder | Eucentric ( SIDE ENTRY, EUCENTRIC ) |
| Tilt Angle | 0 degrees - 0 degrees |
| Camera | |
| Detector | CCD |
| Image Acquisition | |
| Number of Digital Images | 400 |
| Sampling Size | 14.22 microns |
| Quant Bit Number | 12 |
| Details | Images were recorded on CCD, no scanning, sampling step size was adjusted to calibrated image size |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | Projection matching |
| Software | IMAGIC, SPIDER, EMAN |
| Details | Spider option BP 32F Back Projection - 3D, Sampled, Interpolated in Fourier space |
| Resolution By Author | 25 |
| Resolution Method | FSC at 0.5 |
| Single Particle | |
| Number of Projections | 16300 |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-1640.xml (7.9 KB) | ||
|---|---|---|---|
| Map data | emd_1640.map.gz (271.6 KB) | ||
| Images | vatpase_emdb.tif (137.4 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1640 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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