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- EMDB-18124: A cryo-ET study of ciliary rootlet organization - purified rootle... -

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Basic information

Entry
Database: EMDB / ID: EMD-18124
TitleA cryo-ET study of ciliary rootlet organization - purified rootlet example 3
Map datapurified rootlet, eman2 preprocessed cropped tomogram for segmentation. Object files are found on biostudies (S-BSST1164, https://www.ebi.ac.uk/biostudies/studies/S-BSST1164)
Sample
  • Organelle or cellular component: Ciliary rootlet surrounded by cellular membranes
Keywordsciliary rootlet / rootlet / rootletin / centriole / cilia / STRUCTURAL PROTEIN
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
Authorsvan Hoorn C / Carter AP
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_A025_1011 United Kingdom
Wellcome Trust210711/Z/18/Z United Kingdom
CitationJournal: To Be Published
Title: A cryo-ET study of ciliary rootlet organization
Authors: van Hoorn C / Carter AP
History
DepositionAug 3, 2023-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateOct 18, 2023-
Current statusOct 18, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18124.png

Downloads & links

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Map

FileDownload / File: emd_18124.map.gz / Format: CCP4 / Size: 73.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpurified 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 sizeX=Y=Z: 11.104 Å
Density
Minimum - Maximum-3.0 - 3.0
Average (Standard dev.)0.01585852 (±0.92345303)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin170153140
Dimensions48041696
Spacing41648096
CellA: 4619.264 Å / B: 5329.92 Å / C: 1065.984 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Ciliary rootlet surrounded by cellular membranes

EntireName: Ciliary rootlet surrounded by cellular membranes
Components
  • Organelle or cellular component: Ciliary rootlet surrounded by cellular membranes

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Supramolecule #1: Ciliary rootlet surrounded by cellular membranes

SupramoleculeName: 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.
Source (natural)Organism: Mus musculus (house mouse) / Organ: eye / Tissue: retina / Organelle: rootlet / Location in cell: centriole associated, cytoplasm

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: BBI / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 6.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.68 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 41
DetailsFor 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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