+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2094 | |||||||||
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Title | Central hub structure of Trichonympha cartwheel | |||||||||
Map data | Reconstruction of the central hub (cartwheel component) | |||||||||
Sample |
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Keywords | centriole / cartwheel / basal body | |||||||||
Biological species | Trichonympha (eukaryote) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 45.0 Å | |||||||||
Authors | Guichard P / Desfosses A / Maheshwari A / Hachet V / Dietrich C / Brune A / Ishikawa T / Sachse C / Gonczy P | |||||||||
Citation | Journal: Science / Year: 2012 Title: Cartwheel architecture of Trichonympha basal body. Authors: Paul Guichard / Ambroise Desfosses / Aditi Maheshwari / Virginie Hachet / Carsten Dietrich / Andreas Brune / Takashi Ishikawa / Carsten Sachse / Pierre Gönczy / Abstract: Centrioles and basal bodies are essential for the formation of cilia, flagella, and centrosomes. They exhibit a characteristic ninefold symmetry imparted by a cartwheel thought to contain rings of ...Centrioles and basal bodies are essential for the formation of cilia, flagella, and centrosomes. They exhibit a characteristic ninefold symmetry imparted by a cartwheel thought to contain rings of SAS-6 proteins. We used cryoelectron tomography to investigate the architecture of the exceptionally long cartwheel of the flagellate Trichonympha. We found that the cartwheel is a stack of central rings that exhibit a vertical periodicity of 8.5 nanometers and is able to accommodate nine SAS-6 homodimers. The spokes that emanate from two such rings associate into a layer, with a vertical periodicity of 17 nanometers on the cartwheel margin. Thus, by using the power of biodiversity, we unveiled the architecture of the cartwheel at the root of the ninefold symmetry of centrioles and basal bodies. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2094.map.gz | 2 MB | EMDB map data format | |
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Header (meta data) | emd-2094-v30.xml emd-2094.xml | 7.8 KB 7.8 KB | Display Display | EMDB header |
Images | EMD-2094.png | 82.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2094 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2094 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2094.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of the central hub (cartwheel component) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 7.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Trichonympha central hub, central part of the Basal body cartwheel
Entire | Name: Trichonympha central hub, central part of the Basal body cartwheel |
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Components |
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-Supramolecule #1000: Trichonympha central hub, central part of the Basal body cartwheel
Supramolecule | Name: Trichonympha central hub, central part of the Basal body cartwheel type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Centriole
Supramolecule | Name: Centriole / type: organelle_or_cellular_component / ID: 1 / Name.synonym: Basal body / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Trichonympha (eukaryote) / Organelle: Basal body |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
-Sample preparation
Buffer | Details: K-Pipes 10 mM |
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Vitrification | Cryogen name: ETHANE / Instrument: OTHER |
-Electron microscopy
Microscope | JEOL 2200FS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Date | Jul 1, 2011 |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 45.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN, himpose, SPIDER |
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Details | 414 original images (before symmetrization) were included in the final reconstruction. Average number of tilts used in the 3D reconstructions: 414. |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera |
Refinement | Space: REAL |