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- EMDB-10998: Mitochondrial ATP synthase monomer from Rattus norvegicus domestica -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10998 | |||||||||
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Title | Mitochondrial ATP synthase monomer from Rattus norvegicus domestica | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 13.5 Å | |||||||||
![]() | Chesnokov YM / Kamyshinsky RA | |||||||||
![]() | ![]() Title: Determining the Structure and Location of the ATP Synthase in the Membranes of Rat's Heart Mitochondria Using Cryoelectron Tomography Authors: Nesterov SV / Chesnokov YM / Kamyshinsky RA / Yaguzhinsky LS / Vasilov RG | |||||||||
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 | ![]() | 682.9 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.1 KB 16.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 3 KB | Display | ![]() |
Images | ![]() | 34.9 KB | ||
Masks | ![]() | 2 MB | ![]() | |
Others | ![]() ![]() | 1.4 MB 1.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 314.9 KB | Display | ![]() |
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Full document | ![]() | 314.1 KB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 10997 |
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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: 3.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_10998_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_10998_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Mitochondrial ATP synthase dimer from Rattus norvegicus
Entire | Name: Mitochondrial ATP synthase dimer from Rattus norvegicus |
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Components |
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-Supramolecule #1: Mitochondrial ATP synthase dimer from Rattus norvegicus
Supramolecule | Name: Mitochondrial ATP synthase dimer from Rattus norvegicus type: organelle_or_cellular_component / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 600 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | 3D array |
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Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Homemade / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 2.5 seconds. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Spherical aberration corrector: Cs image corrector (CEOS, Germany) |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Average exposure time: 1.5 sec. / Average electron dose: 1.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated magnification: 37837 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 18000 |
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 | PDB ID: |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient |