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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8837 | |||||||||
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Title | Sub-tomogram average of I1 dynein Post class | |||||||||
![]() | Sub-tomogram average of I1 dynein Post class: the two dynein heavy chains of sea urchin sperm flagellar I1 dynein complex are in the post-powerstroke state. | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 41.0 Å | |||||||||
![]() | Lin J / Nicastro D | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Asymmetric distribution and spatial switching of dynein activity generates ciliary motility. Authors: Jianfeng Lin / Daniela Nicastro / ![]() Abstract: Motile cilia and flagella are essential, highly conserved organelles, and their motility is driven by the coordinated activities of multiple dynein isoforms. The prevailing "switch-point" hypothesis ...Motile cilia and flagella are essential, highly conserved organelles, and their motility is driven by the coordinated activities of multiple dynein isoforms. The prevailing "switch-point" hypothesis posits that dyneins are asymmetrically activated to drive flagellar bending. To test this model, we applied cryo-electron tomography to visualize activity states of individual dyneins relative to their locations along beating flagella of sea urchin sperm cells. As predicted, bending was generated by the asymmetric distribution of dynein activity on opposite sides of the flagellum. However, contrary to predictions, most dyneins were in their active state, and the smaller population of conformationally inactive dyneins switched flagellar sides relative to the bending direction. Thus, our data suggest a "switch-inhibition" mechanism in which force imbalance is generated by inhibiting, rather than activating, dyneins on alternating sides of the flagellum. | |||||||||
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 | ![]() | 591.9 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.2 KB 11.2 KB | Display Display | ![]() |
Images | ![]() | 85.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78.1 KB | Display | ![]() |
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Full document | ![]() | 77.2 KB | Display | |
Data in XML | ![]() | 494 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8835C ![]() 8836C ![]() 8838C C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 13.8 Data #1: Tilt series of immotile sea urchin sperm flagella [tilt series]) |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Sub-tomogram average of I1 dynein Post class: the two dynein heavy chains of sea urchin sperm flagellar I1 dynein complex are in the post-powerstroke state. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 9.856 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 : Sea urchin sperm
Entire | Name: Sea urchin sperm |
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Components |
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-Supramolecule #1: Sea urchin sperm
Supramolecule | Name: Sea urchin sperm / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: Sperm were diluted in demembranation buffer (30 mM HEPES, pH 8.0, 150 mM KCl, 4 mM MgCl2, 0.5 mM EGTA, 0.1% Triton X-100) and incubated for one minute to remove the flagellar membrane. The ...Details: Sperm were diluted in demembranation buffer (30 mM HEPES, pH 8.0, 150 mM KCl, 4 mM MgCl2, 0.5 mM EGTA, 0.1% Triton X-100) and incubated for one minute to remove the flagellar membrane. The sperm were then collected by centrifugation at 1000x g, and resuspended in demembranation buffer (but without Triton X-100). |
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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: 8 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
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Electron microscopy
Microscope | FEI TECNAI F30 |
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Specialist optics | Energy filter - Name: GIF |
Image recording | Film or detector model: GATAN MULTISCAN / Average electron dose: 1.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 13500 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 41.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET (ver. 1.9.0) / Number subtomograms used: 392 |
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Extraction | Number tomograms: 7 / Number images used: 1134 / Software - Name: PEET (ver. 1.9.0) |
Final 3D classification | Software - Name: PEET (ver. 1.9.0) |
Final angle assignment | Type: OTHER |