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- EMDB-46485: Cryo-electron tomography and subtomogram averaging of AK1-/- mous... -
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Open data
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Basic information
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Title | Cryo-electron tomography and subtomogram averaging of AK1-/- mouse respiratory ciliary axoneme | ||||||||||||
![]() | Cryo-electron tomography and subtomogram averaging of AK1-/- mouse respiratory ciliary axoneme | ||||||||||||
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![]() | axoneme / radial spoke / STRUCTURAL PROTEIN | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 44.0 Å | ||||||||||||
![]() | Yanhe Z / Xuewu Z / Daniela N | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The cryo-EM structure of mouse radial spoke 3 reveals a unique metabolic and regulatory hub in cilia Authors: Yanhe Z / Xuewu Z / Daniela N | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.8 KB 15.8 KB | Display Display | ![]() |
Images | ![]() | 45.6 KB | ||
Filedesc metadata | ![]() | 4.5 KB | ||
Others | ![]() ![]() | 4.2 MB 4.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 764.9 KB | Display | ![]() |
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Full document | ![]() | 764.4 KB | Display | |
Data in XML | ![]() | 7.2 KB | Display | |
Data in CIF | ![]() | 9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Cryo-electron tomography and subtomogram averaging of AK1-/- mouse respiratory ciliary axoneme | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 10.77 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half maps are unwindowed, they need to be...
File | emd_46485_half_map_1.map | ||||||||||||
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Annotation | Half maps are unwindowed, they need to be windowed, tapered, masked or etc. before FSC calculation. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half maps are unwindowed, they need to be...
File | emd_46485_half_map_2.map | ||||||||||||
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Annotation | Half maps are unwindowed, they need to be windowed, tapered, masked or etc. before FSC calculation. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Respiratory ciliary axonemes from mouse
Entire | Name: Respiratory ciliary axonemes from mouse |
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Components |
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-Supramolecule #1: Respiratory ciliary axonemes from mouse
Supramolecule | Name: Respiratory ciliary axonemes from mouse / type: organelle_or_cellular_component / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | cell |
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Sample preparation
Buffer | pH: 7.4 Details: 30 mM HEPES pH 7.4, 25 mM KCl, 5 mM MgSO4, 1 mM EGTA, 0.1 mM EDTA |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TECNAI F30 |
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Image recording | Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Average electron dose: 1.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 8.0 µm / Nominal magnification: 13500 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 44.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 900 |
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Extraction | Number tomograms: 9 / Number images used: 1205 |
CTF correction | Type: NONE |
Final angle assignment | Type: OTHER / Software - Name: PEET (ver. 1.10.0) Details: angles (and shifts) for each subvolume are assigned by maximizing normalized cross-correlation between the subvolume and the reference |