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- EMDB-18125: A cryo-ET study of ciliary rootlet organization - purified rootle... -
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Open data
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Basic information
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Title | A cryo-ET study of ciliary rootlet organization - purified rootlet example 4 | |||||||||
![]() | purified rootlet, eman2 preprocessed cropped tomogram for segmentation. Object files are found on biostudies (S-BSST1164, https://www.ebi.ac.uk/biostudies/studies/S-BSST1164) | |||||||||
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![]() | ciliary rootlet / rootlet / rootletin / centriole / cilia / STRUCTURAL PROTEIN | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | electron tomography / cryo EM | |||||||||
![]() | van Hoorn C / Carter AP | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A cryo-ET study of ciliary rootlet organization Authors: van Hoorn C / Carter AP | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 108.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 8.1 KB 8.1 KB | Display Display | ![]() |
Images | ![]() | 114.3 KB | ||
Filedesc metadata | ![]() | 4.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 461.2 KB | Display | ![]() |
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Full document | ![]() | 460.8 KB | Display | |
Data in XML | ![]() | 3.9 KB | Display | |
Data in CIF | ![]() | 4.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | purified rootlet, eman2 preprocessed cropped tomogram for segmentation. Object files are found on biostudies (S-BSST1164, https://www.ebi.ac.uk/biostudies/studies/S-BSST1164) | ||||||||||||||||||||
Voxel size | X=Y=Z: 11.104 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : Ciliary rootlet surrounded by cellular membranes
Entire | Name: Ciliary rootlet surrounded by cellular membranes |
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Components |
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-Supramolecule #1: Ciliary rootlet surrounded by cellular membranes
Supramolecule | Name: Ciliary rootlet surrounded by cellular membranes / type: organelle_or_cellular_component / ID: 1 / Parent: 0 Details: The sample was purified according to https://doi.org/10.1016/j.cell.2012.10.038, maintaining cellular interactions with the rootlet. |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | electron tomography |
Aggregation state | cell |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: BBI / Diameter: 10 nm |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.68 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Details | For tomogram segmentation, tomograms were reconstructed as even/odd frame half tomograms using the above mentioned WARP pipeline and denoised using Noise2Map(Tegunov & Cramer, 2018). The tomograms were then deconvolved and isotropically reconstructed with denoising using IsoNet(Liu et al, 2021) with a cube size of 128 pixels. The tomograms were then preprocessed in EMAN2.2 for training of the TomoSeg CNN(Chen et al, 2017). |
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Final reconstruction | Number images used: 41 |