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Yorodumi- EMDB-7777: Distal domain, triplet-microtubule map from a Chinese hamster ova... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7777 | |||||||||
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Title | Distal domain, triplet-microtubule map from a Chinese hamster ovary (CHO) centriole | |||||||||
Map data | primary map | |||||||||
Sample |
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Biological species | Cricetulus griseus (Chinese hamster) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 25.0 Å | |||||||||
Authors | Agard DA / Greenan GA | |||||||||
Citation | Journal: Elife / Year: 2018 Title: Insights into centriole geometry revealed by cryotomography of doublet and triplet centrioles. Authors: Garrett A Greenan / Bettina Keszthelyi / Ronald D Vale / David A Agard / Abstract: Centrioles are cylindrical assemblies comprised of 9 singlet, doublet, or triplet microtubules, essential for the formation of motile and sensory cilia. While the structure of the cilium is being ...Centrioles are cylindrical assemblies comprised of 9 singlet, doublet, or triplet microtubules, essential for the formation of motile and sensory cilia. While the structure of the cilium is being defined at increasing resolution, centriolar structure remains poorly understood. Here, we used electron cryo-tomography to determine the structure of mammalian (triplet) and (doublet) centrioles. Mammalian centrioles have two distinct domains: a 200 nm proximal core region connected by A-C linkers, and a distal domain where the C-tubule is incomplete and a pair of novel linkages stabilize the assembly producing a geometry more closely resembling the ciliary axoneme. centrioles resemble the mammalian core, but with their doublet microtubules linked through the A tubules. The commonality of core-region length, and the abrupt transition in mammalian centrioles, suggests a conserved length-setting mechanism. The unexpected linker diversity suggests how unique centriolar architectures arise in different tissues and organisms. | |||||||||
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_7777.map.gz | 1.4 MB | EMDB map data format | |
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Header (meta data) | emd-7777-v30.xml emd-7777.xml | 7.3 KB 7.3 KB | Display Display | EMDB header |
Images | emd_7777.png | 86.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7777 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7777 | HTTPS FTP |
-Validation report
Summary document | emd_7777_validation.pdf.gz | 77.5 KB | Display | EMDB validaton report |
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Full document | emd_7777_full_validation.pdf.gz | 76.5 KB | Display | |
Data in XML | emd_7777_validation.xml.gz | 492 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7777 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7777 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_7777.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | primary map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 8.18 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 : Distal domain, triplet-microtubule map from a Chinese hamster ova...
Entire | Name: Distal domain, triplet-microtubule map from a Chinese hamster ovary (CHO) centriole |
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Components |
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-Supramolecule #1: Distal domain, triplet-microtubule map from a Chinese hamster ova...
Supramolecule | Name: Distal domain, triplet-microtubule map from a Chinese hamster ovary (CHO) centriole type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Cricetulus griseus (Chinese hamster) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 8.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1000 |
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Extraction | Number tomograms: 9 / Number images used: 1000 |
Final angle assignment | Type: ANGULAR RECONSTITUTION |