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- EMDB-6520: Structure and function of outer dynein intermediate and light cha... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6520 | |||||||||
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Title | Structure and function of outer dynein intermediate and light chain complex | |||||||||
![]() | Streptavidin-labeled IC2M549BCCP axoneme | |||||||||
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![]() | cilia and flagella / axoneme / outer dynein arm / intermediate chain / light chain | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 48.0 Å | |||||||||
![]() | Oda T / Abe T / Yanagisawa H / Kikkawa M | |||||||||
![]() | ![]() Title: Structure and function of outer dynein arm intermediate and light chain complex. Authors: Toshiyuki Oda / Tatsuki Abe / Haruaki Yanagisawa / Masahide Kikkawa / ![]() Abstract: The outer dynein arm (ODA) is a molecular complex that drives the beating motion of cilia/flagella. Chlamydomonas ODA is composed of three heavy chains (HCs), two ICs, and 11 light chains (LCs). ...The outer dynein arm (ODA) is a molecular complex that drives the beating motion of cilia/flagella. Chlamydomonas ODA is composed of three heavy chains (HCs), two ICs, and 11 light chains (LCs). Although the three-dimensional (3D) structure of the whole ODA complex has been investigated, the 3D configurations of the ICs and LCs are largely unknown. Here we identified the 3D positions of the two ICs and three LCs using cryo-electron tomography and structural labeling. We found that these ICs and LCs were all localized at the root of the outer-inner dynein (OID) linker, designated the ODA-Beak complex. Of interest, the coiled-coil domain of IC2 extended from the ODA-Beak to the outer surface of ODA. Furthermore, we investigated the molecular mechanisms of how the OID linker transmits signals to the ODA-Beak, by manipulating the interaction within the OID linker using a chemically induced dimerization system. We showed that the cross-linking of the OID linker strongly suppresses flagellar motility in vivo. These results suggest that the ICs and LCs of the ODA form the ODA-Beak, which may be involved in mechanosignaling from the OID linker to the HCs. | |||||||||
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 | ![]() | 16.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 8.5 KB 8.5 KB | Display Display | ![]() |
Images | ![]() ![]() | 45.8 KB 3.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78.2 KB | Display | ![]() |
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Full document | ![]() | 77.3 KB | Display | |
Data in XML | ![]() | 494 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6515C ![]() 6516C ![]() 6517C ![]() 6518C ![]() 6519C ![]() 6521C ![]() 6522C ![]() 6523C ![]() 6524C 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 IC2M549BCCP 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 IC2M549BCCP axoneme
Entire | Name: Streptavidin-labeled IC2M549BCCP axoneme |
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Components |
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-Supramolecule #1000: Streptavidin-labeled IC2M549BCCP axoneme
Supramolecule | Name: Streptavidin-labeled IC2M549BCCP 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 | Jun 7, 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: 48.0 Å / Resolution method: OTHER / Software - Name: IMOD, PEET / Number subtomograms used: 1168 |