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- EMDB-2118: Cryo-electron tomography averaged map of microtubule doublet 9 in... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2118 | |||||||||
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Title | Cryo-electron tomography averaged map of microtubule doublet 9 in the distal/central region of Chlamydomonas axoneme | |||||||||
![]() | Reconstruction of outer doublet 9 of the Chlamydomonas axoneme in the distal/central region. | |||||||||
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![]() | axoneme / dynein / Chlamydomonas / microtubule doublet | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 47.0 Å | |||||||||
![]() | Bui KH / Yagi T / Yamamoto R / Kamiya R / Ishikawa T | |||||||||
![]() | ![]() Title: Polarity and asymmetry in the arrangement of dynein and related structures in the Chlamydomonas axoneme. Authors: Khanh Huy Bui / Toshiki Yagi / Ryosuke Yamamoto / Ritsu Kamiya / Takashi Ishikawa / ![]() Abstract: Understanding the molecular architecture of the flagellum is crucial to elucidate the bending mechanism produced by this complex organelle. The current known structure of the flagellum has not yet ...Understanding the molecular architecture of the flagellum is crucial to elucidate the bending mechanism produced by this complex organelle. The current known structure of the flagellum has not yet been fully correlated with the complex composition and localization of flagellar components. Using cryoelectron tomography and subtomogram averaging while distinguishing each one of the nine outer doublet microtubules, we systematically collected and reconstructed the three-dimensional structures in different regions of the Chlamydomonas flagellum. We visualized the radial and longitudinal differences in the flagellum. One doublet showed a distinct structure, whereas the other eight were similar but not identical to each other. In the proximal region, some dyneins were missing or replaced by minor dyneins, and outer-inner arm dynein links were variable among different microtubule doublets. These findings shed light on the intricate organization of Chlamydomonas flagella, provide clues to the mechanism that produces asymmetric flagellar beating, and pose a new challenge for the functional study of the flagella. | |||||||||
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 | ![]() | 25.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.1 KB 10.1 KB | Display Display | ![]() |
Images | ![]() | 191.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2113C ![]() 2114C ![]() 2115C ![]() 2116C ![]() 2117C ![]() 2119C ![]() 2120C ![]() 2121C ![]() 2122C ![]() 2123C ![]() 2124C ![]() 2125C ![]() 2126C ![]() 2127C ![]() 2128C ![]() 2129C ![]() 2130C ![]() 2131C ![]() 2132C 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 | Reconstruction of outer doublet 9 of the Chlamydomonas axoneme in the distal/central region. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 7.25 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 : Outer doublet 9 of Chlamydomonas axoneme in the distal/central region
Entire | Name: Outer doublet 9 of Chlamydomonas axoneme in the distal/central region |
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Components |
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-Supramolecule #1000: Outer doublet 9 of Chlamydomonas axoneme in the distal/central region
Supramolecule | Name: Outer doublet 9 of Chlamydomonas axoneme in the distal/central region type: sample / ID: 1000 / Details: Flagella were isolated from Chlamydomonas. / Number unique components: 1 |
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-Supramolecule #1: flagellum
Supramolecule | Name: flagellum / type: organelle_or_cellular_component / ID: 1 / Name.synonym: axoneme,cilia / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
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Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.4 Details: 30 mM Hepes, pH 7.4, 5 mM MgSO4, 1 mM DTT, 0.5 mM EDTA, 25 mM KCl, and 0.5% (wt/vol) polyethylene glycol (MW 20,000) |
Grid | Details: 300 mesh Quantifoil Holey Carbon copper grid R2/1 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 110 K / Instrument: FEI VITROBOT MARK II / Method: Offset -3, blot 3 seconds, drain time 0 second |
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Electron microscopy
Microscope | FEI TECNAI 20 |
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Temperature | Min: 93 K / Max: 118 K / Average: 98 K |
Specialist optics | Energy filter - Name: Gatan Tridem / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Date | Nov 26, 2010 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Number real images: 536 / Average electron dose: 60 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 19303 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 27500 |
Sample stage | Specimen holder: Gatan 626, liquid nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° |
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Image processing
Details | R-weighted back projection using IMOD with fiducial markers. Average number of tilts used in the 3D reconstructions: 61. Average tomographic tilt angle increment: 2. |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 47.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD, BSOFT, SPIDER, TOM, package, Matlab |