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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6312 | |||||||||
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Title | Ciliary microtubule doublet by single particle analysis | |||||||||
![]() | Ciliary microtubule doublet | |||||||||
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![]() | cilia / microtubule / tubulin / dynein | |||||||||
Function / homology | ![]() microtubule-based process / structural constituent of cytoskeleton / microtubule / GTPase activity / GTP binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 23.0 Å | |||||||||
![]() | Maheshwari A / Obbineni JM / Bui KH / Shibata K / Toyoshima Y / Ishikawa T | |||||||||
![]() | ![]() Title: α- and β-Tubulin Lattice of the Axonemal Microtubule Doublet and Binding Proteins Revealed by Single Particle Cryo-Electron Microscopy and Tomography. Authors: Aditi Maheshwari / Jagan Mohan Obbineni / Khanh Huy Bui / Keitaro Shibata / Yoko Y Toyoshima / Takashi Ishikawa / ![]() ![]() Abstract: Microtubule doublet (MTD) is the main skeleton of cilia/flagella. Many proteins, such as dyneins and radial spokes, bind to MTD, and generate or regulate force. While the structure of the ...Microtubule doublet (MTD) is the main skeleton of cilia/flagella. Many proteins, such as dyneins and radial spokes, bind to MTD, and generate or regulate force. While the structure of the reconstituted microtubule has been solved at atomic resolution, nature of the axonemal MTD is still unclear. There are a few hypotheses of the lattice arrangement of its α- and β-tubulins, but it has not been described how dyneins and radial spokes bind to MTD. In this study, we analyzed the three-dimensional structure of Tetrahymena MTD at ∼19 Å resolution by single particle cryo-electron microscopy. To identify α- and β-tubulins, we combined image analysis of MTD with specific kinesin decoration. This work reveals that α- and β-tubulins form a B-lattice arrangement in the entire MTD with a seam at the outer junction. We revealed the unique way in which inner arm dyneins, radial spokes, and proteins inside MTD bind and bridge protofilaments. | |||||||||
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 | ![]() | 17 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.6 KB 10.6 KB | Display Display | ![]() |
Images | ![]() ![]() | 35.1 KB 3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3jaoMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Ciliary microtubule doublet | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.478 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 : microtubule doublet from Tetrahymena cilia
Entire | Name: microtubule doublet from Tetrahymena cilia |
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Components |
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-Supramolecule #1000: microtubule doublet from Tetrahymena cilia
Supramolecule | Name: microtubule doublet from Tetrahymena cilia / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: cilium
Supramolecule | Name: cilium / type: organelle_or_cellular_component / ID: 1 / Name.synonym: flagellum Details: Microtubule doublets were prepared from Tetrahymena cilia. Number of copies: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 7.4 Details: 30 mM HEPES, pH 7.4, 5 mM MgSO4, 1 mM DTT, 0.5 mM EDTA, 25 mM KCl, 4 mM CaCl2 |
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Grid | Details: 300 mesh copper grid with holey carbon film, glow discharged |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK II / Method: Blot for 3 seconds before plunging. |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Min: 80 K / Max: 100 K / Average: 90 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification. |
Specialist optics | Energy filter - Name: GIF Trideem / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 25.0 eV |
Date | Oct 25, 2011 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 30 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.5 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 67000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 9.0 Å Applied symmetry - Helical parameters - Δ&Phi: 28.0 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: OTHER / Software - Name: Spider / Number images used: 10700 |