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- EMDB-9169: Electron cryo-tomography and subtomogram averaging of microtubule... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9169 | |||||||||||||||
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Title | Electron cryo-tomography and subtomogram averaging of microtubule triplet from procentriole | |||||||||||||||
![]() | a subtomogram average of the B-tubule in procentriole from Chlamydomonas Reinhardtii | |||||||||||||||
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Biological species | ![]() ![]() | |||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 22.3 Å | |||||||||||||||
![]() | Li S / Fernandez JJ / Marshall W / Agard DA | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Electron cryo-tomography provides insight into procentriole architecture and assembly mechanism. Authors: Sam Li / Jose-Jesus Fernandez / Wallace F Marshall / David A Agard / ![]() ![]() Abstract: Centriole is an essential structure with multiple functions in cellular processes. Centriole biogenesis and homeostasis is tightly regulated. Using electron cryo-tomography (cryoET) we present the ...Centriole is an essential structure with multiple functions in cellular processes. Centriole biogenesis and homeostasis is tightly regulated. Using electron cryo-tomography (cryoET) we present the structure of procentrioles from . We identified a set of non-tubulin components attached to the triplet microtubule (MT), many are at the junctions of tubules likely to reinforce the triplet. We describe structure of the A-C linker that bridges neighboring triplets. The structure infers that POC1 is likely an integral component of A-C linker. Its conserved WD40 β-propeller domain provides attachment sites for other A-C linker components. The twist of A-C linker results in an iris diaphragm-like motion of the triplets in the longitudinal direction of procentriole. Finally, we identified two assembly intermediates at the growing ends of procentriole allowing us to propose a model for the procentriole assembly. Our results provide a comprehensive structural framework for understanding the molecular mechanisms underpinning procentriole biogenesis and assembly. | |||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 6.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.2 KB 9.2 KB | Display Display | ![]() |
Images | ![]() | 75.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 80.9 KB | Display | ![]() |
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Full document | ![]() | 80.1 KB | Display | |
Data in XML | ![]() | 494 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9167C ![]() 9168C ![]() 9170C ![]() 9171C ![]() 9172C ![]() 9173C ![]() 9174C C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | a subtomogram average of the B-tubule in procentriole from Chlamydomonas Reinhardtii | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.82 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Centriole
Entire | Name: Centriole |
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Components |
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-Supramolecule #1: Centriole
Supramolecule | Name: Centriole / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Details: isolated centriole and procentriole |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | cell |
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Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-5 / Average exposure time: 1.0 sec. / Average electron dose: 0.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 22.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 12179 |
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Extraction | Number tomograms: 193 / Number images used: 12937 |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Crystal parameters | Unit cell - A: 578.4 Å / Unit cell - B: 578.4 Å / Unit cell - C: 578.4 Å / Unit cell - γ: 90 ° / Unit cell - α: 90 ° / Unit cell - β: 90 ° / Space group: C1 |