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Yorodumi- EMDB-2329: electron cryo-tomography reconstruction and subvolume averaging o... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2329 | |||||||||
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Title | electron cryo-tomography reconstruction and subvolume averaging of the Trichonympha proximal basal body | |||||||||
Map data | Trichonympha cartwheel map at 38A resolution | |||||||||
Sample |
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Keywords | microtubule triplet / Trichonympha / basal body / centriole / centrosome / cartwheel | |||||||||
Biological species | Trichonympha (eukaryote) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 38.0 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_2329.map.gz | 8.4 MB | EMDB map data format | |
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Header (meta data) | emd-2329-v30.xml emd-2329.xml | 8.2 KB 8.2 KB | Display Display | EMDB header |
Images | emd_2329.png | 163.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2329 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2329 | HTTPS FTP |
-Validation report
Summary document | emd_2329_validation.pdf.gz | 192.2 KB | Display | EMDB validaton report |
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Full document | emd_2329_full_validation.pdf.gz | 191.3 KB | Display | |
Data in XML | emd_2329_validation.xml.gz | 4.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2329 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2329 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2329.map.gz / Format: CCP4 / Size: 10 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Trichonympha cartwheel map at 38A resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 trichonympha basal body
Entire | Name: Isolated trichonympha basal body |
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Components |
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-Supramolecule #1000: Isolated trichonympha basal body
Supramolecule | Name: Isolated trichonympha basal body / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Basal body
Supramolecule | Name: Basal body / type: organelle_or_cellular_component / ID: 1 / Name.synonym: Centriole / Recombinant expression: No |
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Source (natural) | Organism: Trichonympha (eukaryote) / synonym: Trichonympha / Organelle: centriole / Location in cell: cytoplasmic |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 / Details: K-Pipes 10 mM |
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Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Method: Blot for 1 seconds before plunging |
-Electron microscopy
Microscope | FEI TECNAI 20 |
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Date | Jul 1, 2012 |
Image recording | Number real images: 100 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 29000 |
Sample stage | Specimen holder model: OTHER / Tilt series - Axis1 - Min angle: 65 ° / Tilt series - Axis1 - Max angle: 65 ° |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 38.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD, Spider, bsoft Details: Final maps were calculated from six different tomograms Number subtomograms used: 600 |
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Final 3D classification | Number classes: 1 |