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Yorodumi- EMDB-11049: Electron cryo-tomography reconstruction and subvolume averaging o... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11049 | |||||||||
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Title | Electron cryo-tomography reconstruction and subvolume averaging of the proximal basal body triplet from Trichonympha | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Trichonympha sp. (eukaryote) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 42.0 Å | |||||||||
Authors | Guichard P / Hachet V / Majubu N / Neves A / Demurtas D / Olieric N / Fluckiger I / Yamada A / Kihara K / Nishida Y ...Guichard P / Hachet V / Majubu N / Neves A / Demurtas D / Olieric N / Fluckiger I / Yamada A / Kihara K / Nishida Y / Moriya S / Steinmetz MO / Hongoh Y / Gonczy P | |||||||||
Citation | Journal: Curr Biol / Year: 2013 Title: Native architecture of the centriole proximal region reveals features underlying its 9-fold radial symmetry. Authors: Paul Guichard / Virginie Hachet / Norbert Majubu / Aitana Neves / Davide Demurtas / Natacha Olieric / Isabelle Fluckiger / Akinori Yamada / Kumiko Kihara / Yuichiro Nishida / Shigeharu ...Authors: Paul Guichard / Virginie Hachet / Norbert Majubu / Aitana Neves / Davide Demurtas / Natacha Olieric / Isabelle Fluckiger / Akinori Yamada / Kumiko Kihara / Yuichiro Nishida / Shigeharu Moriya / Michel O Steinmetz / Yuichi Hongoh / Pierre Gönczy / Abstract: BACKGROUND: Centrioles are cylindrical microtubule-based structures whose assembly is critical for the formation of cilia, flagella, and centrosomes. The centriole proximal region harbors a cartwheel ...BACKGROUND: Centrioles are cylindrical microtubule-based structures whose assembly is critical for the formation of cilia, flagella, and centrosomes. The centriole proximal region harbors a cartwheel that dictates the 9-fold symmetry of centrioles. Although the cartwheel architecture has been recently analyzed, how it connects to the peripheral microtubules is not understood. More generally, a high-resolution view of the proximal region of the centriole is lacking, thus limiting understanding of the underlying assembly mechanisms. RESULTS: We report the complete architecture of the Trichonympha centriole proximal region using cryotomography. The resulting 3D map reveals several features, including additional densities in the ...RESULTS: We report the complete architecture of the Trichonympha centriole proximal region using cryotomography. The resulting 3D map reveals several features, including additional densities in the cartwheel that exhibit a 9-fold symmetrical arrangement, as well as the structure of the Pinhead and the A-C linker that connect to microtubules. Moreover, we uncover striking chiral features that might impart directionality to the entire centriole. Furthermore, we identify Trichonympha SAS-6 and demonstrate that it localizes to the cartwheel in vivo. CONCLUSIONS: Our work provides unprecedented insight into the architecture of the centriole proximal region, which is key for a thorough understanding of the mechanisms governing centriole assembly. | |||||||||
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_11049.map.gz | 3 MB | EMDB map data format | |
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Header (meta data) | emd-11049-v30.xml emd-11049.xml | 8.9 KB 8.9 KB | Display Display | EMDB header |
Images | emd_11049.png | 32.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11049 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11049 | HTTPS FTP |
-Validation report
Summary document | emd_11049_validation.pdf.gz | 215.7 KB | Display | EMDB validaton report |
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Full document | emd_11049_full_validation.pdf.gz | 214.9 KB | Display | |
Data in XML | emd_11049_validation.xml.gz | 4.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11049 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11049 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_11049.map.gz / Format: CCP4 / Size: 3.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 7.5 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 : Isolated Trichonmypha centriole
Entire | Name: Isolated Trichonmypha centriole |
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Components |
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-Supramolecule #1: Isolated Trichonmypha centriole
Supramolecule | Name: Isolated Trichonmypha centriole / type: organelle_or_cellular_component / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Trichonympha sp. (eukaryote) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TECNAI 20 |
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Image recording | Film or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 80.0 e/Å2 / Details: binning 2, 0.748 nm final pixel size |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
-Image processing
Final reconstruction | Applied symmetry - Point group: C9 (9 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 42.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 6000 |
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Extraction | Number tomograms: 6 / Number images used: 6000 |
Final angle assignment | Type: NOT APPLICABLE |