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- EMDB-6510: Docking complex-independent alignment of outer dynein arms with 2... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6510 | |||||||||
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Title | Docking complex-independent alignment of outer dynein arms with 24-nm periodicity | |||||||||
![]() | Streptavidin-labeled DC2-M412BCCP axoneme | |||||||||
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![]() | cilia and flagella / axoneme / outer dynein arm / docking complex | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 47.0 Å | |||||||||
![]() | Oda T / Abe T / Yanagisawa H / Kikkawa M | |||||||||
![]() | ![]() Title: Docking-complex-independent alignment of Chlamydomonas outer dynein arms with 24-nm periodicity in vitro. Authors: Toshiyuki Oda / Tatsuki Abe / Haruaki Yanagisawa / Masahide Kikkawa / ![]() Abstract: The docking complex is a molecular complex necessary for assembly of outer dynein arms (ODAs) on the axonemal doublet microtubules (DMTs) in cilia and flagella. The docking complex is hypothesized to ...The docking complex is a molecular complex necessary for assembly of outer dynein arms (ODAs) on the axonemal doublet microtubules (DMTs) in cilia and flagella. The docking complex is hypothesized to be a 24-nm molecular ruler because ODAs align along the DMTs with 24-nm periodicity. In this study, we rigorously tested this hypothesis using structural and genetic methods. We found that the ODAs can bind to DMTs and porcine microtubules with 24-nm periodicities even in the absence of the docking complexin vitro Using cryo-electron tomography and structural labeling, we observed that the docking complex took an unexpectedly flexible conformation and did not lie along the length of DMTs. In the absence of docking complex, ODAs were released from the DMT at relatively low ionic strength conditions, suggesting that the docking complex strengthens the electrostatic interactions between the ODA and DMT. Based on these results, we conclude that the docking complex serves as a flexible stabilizer of the ODA rather than as a molecular ruler. | |||||||||
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 | ![]() | 985.1 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 8.6 KB 8.6 KB | Display Display | ![]() |
Images | ![]() ![]() | 53.5 KB 4.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6504C ![]() 6505C ![]() 6506C ![]() 6507C ![]() 6508C ![]() 6509C ![]() 6511C 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 | Streptavidin-labeled DC2-M412BCCP axoneme | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.07 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 : Streptavidin-labeled ODA structure from DC2-M412BCCP axoneme
Entire | Name: Streptavidin-labeled ODA structure from DC2-M412BCCP axoneme |
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Components |
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-Supramolecule #1000: Streptavidin-labeled ODA structure from DC2-M412BCCP axoneme
Supramolecule | Name: Streptavidin-labeled ODA structure from DC2-M412BCCP axoneme type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: axoneme
Supramolecule | Name: axoneme / type: organelle_or_cellular_component / ID: 1 / 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 |
Aggregation state | cell |
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Sample preparation
Concentration | 0.01 mg/mL |
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Buffer | pH: 7.2 Details: 30 mM Hepes-NaOH pH 7.2, 5 mM MgCl2, 1 mM dithiothreitol, 1 mM EGTA, 50 mM K-acetate |
Grid | Details: 300 mesh copper grid, holey carbon |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 93 K / Instrument: LEICA EM GP / Method: Blot for 5 seconds before plunging |
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Electron microscopy
Microscope | OTHER |
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Specialist optics | Energy filter - Name: Omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Date | Feb 20, 2015 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 100 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 9.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 25700 |
Sample stage | 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 | Number of tilts (projections) used in 3D reconstruction: 60 Tomographic tilt angle increment: 2 |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 47.0 Å / Resolution method: OTHER / Software - Name: IMOD, PEET / Number subtomograms used: 936 |