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Yorodumi- EMDB-6515: Structure and function of outer dynein intermediate and light cha... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6515 | |||||||||
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Title | Structure and function of outer dynein intermediate and light chain complex | |||||||||
Map data | Streptavidin-labeled IC1M31BCCP axoneme | |||||||||
Sample |
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Keywords | cilia and flagella / axoneme / outer dynein arm / intermediate chain / light chain | |||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 47.0 Å | |||||||||
Authors | Oda T / Abe T / Yanagisawa H / Kikkawa M | |||||||||
Citation | Journal: Mol Biol Cell / Year: 2016 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6515.map.gz | 16.3 MB | EMDB map data format | |
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Header (meta data) | emd-6515-v30.xml emd-6515.xml | 8.5 KB 8.5 KB | Display Display | EMDB header |
Images | 400_6515.gif 80_6515.gif | 55 KB 4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6515 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6515 | HTTPS FTP |
-Validation report
Summary document | emd_6515_validation.pdf.gz | 78.1 KB | Display | EMDB validaton report |
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Full document | emd_6515_full_validation.pdf.gz | 77.2 KB | Display | |
Data in XML | emd_6515_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6515 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6515 | HTTPS FTP |
-Related structure data
Related structure data | 6516C 6517C 6518C 6519C 6520C 6521C 6522C 6523C 6524C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6515.map.gz / Format: CCP4 / Size: 19 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Streptavidin-labeled IC1M31BCCP axoneme | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : Streptavidin-labeled IC1M31BCCP axoneme
Entire | Name: Streptavidin-labeled IC1M31BCCP axoneme |
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Components |
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-Supramolecule #1000: Streptavidin-labeled IC1M31BCCP axoneme
Supramolecule | Name: Streptavidin-labeled IC1M31BCCP 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: Chlamydomonas reinhardtii (plant) / Organelle: flagella |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-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 |
-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 12, 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: FIELD EMISSION GUN |
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 ° |
-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: 848 |