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Yorodumi- EMDB-23926: The structure of the Tetrahymena thermophila outer dynein arm on ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23926 | |||||||||
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Title | The structure of the Tetrahymena thermophila outer dynein arm on doublet microtubule | |||||||||
Map data | ||||||||||
Sample |
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Keywords | cilia / doublet / axoneme / outer dynein arm / dynein / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information outer dynein arm / outer dynein arm assembly / dynein light chain binding / cilium movement / dynein heavy chain binding / axonemal dynein complex / dynein complex / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex ...outer dynein arm / outer dynein arm assembly / dynein light chain binding / cilium movement / dynein heavy chain binding / axonemal dynein complex / dynein complex / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / motile cilium / dynein intermediate chain binding / microtubule-based movement / microtubule-based process / protein-disulfide reductase activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / cilium / microtubule cytoskeleton organization / mitotic cell cycle / microtubule / hydrolase activity / GTPase activity / centrosome / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Tetrahymena thermophila CU428 (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.0 Å | |||||||||
Authors | Kubo S / Yang SK / Ichikawa M / Bui KH | |||||||||
Funding support | Canada, 2 items
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Citation | Journal: EMBO Rep / Year: 2021 Title: Remodeling and activation mechanisms of outer arm dyneins revealed by cryo-EM. Authors: Shintaroh Kubo / Shun Kai Yang / Corbin S Black / Daniel Dai / Melissa Valente-Paterno / Jacek Gaertig / Muneyoshi Ichikawa / Khanh Huy Bui / Abstract: Cilia are thin microtubule-based protrusions of eukaryotic cells. The swimming of ciliated protists and sperm cells is propelled by the beating of cilia. Cilia propagate the flow of mucus in the ...Cilia are thin microtubule-based protrusions of eukaryotic cells. The swimming of ciliated protists and sperm cells is propelled by the beating of cilia. Cilia propagate the flow of mucus in the trachea and protect the human body from viral infections. The main force generators of ciliary beating are the outer dynein arms (ODAs) which attach to the doublet microtubules. The bending of cilia is driven by the ODAs' conformational changes caused by ATP hydrolysis. Here, we report the native ODA complex structure attaching to the doublet microtubule by cryo-electron microscopy. The structure reveals how the ODA complex is attached to the doublet microtubule via the docking complex in its native state. Combined with coarse-grained molecular dynamic simulations, we present a model of how the attachment of the ODA to the doublet microtubule induces remodeling and activation of the ODA complex. | |||||||||
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_23926.map.gz | 5.8 MB | EMDB map data format | |
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Header (meta data) | emd-23926-v30.xml emd-23926.xml | 52.2 KB 52.2 KB | Display Display | EMDB header |
Images | emd_23926.png | 93.1 KB | ||
Filedesc metadata | emd-23926.cif.gz | 18.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23926 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23926 | HTTPS FTP |
-Validation report
Summary document | emd_23926_validation.pdf.gz | 450 KB | Display | EMDB validaton report |
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Full document | emd_23926_full_validation.pdf.gz | 449.6 KB | Display | |
Data in XML | emd_23926_validation.xml.gz | 4.7 KB | Display | |
Data in CIF | emd_23926_validation.cif.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23926 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23926 | HTTPS FTP |
-Related structure data
Related structure data | 7moqMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23926.map.gz / Format: CCP4 / Size: 6.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 2.73 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 : Outer dynein arm complex from Tetrahymena thermophila
+Supramolecule #1: Outer dynein arm complex from Tetrahymena thermophila
+Macromolecule #1: Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protei...
+Macromolecule #2: Outer arm dynein beta heavy chain
+Macromolecule #3: Dynein heavy chain, outer arm protein
+Macromolecule #4: Dynein intermediate chain 2
+Macromolecule #5: Flagellar outer dynein arm intermediate protein, putative
+Macromolecule #6: Dynein light chain roadblock-type 2 protein
+Macromolecule #7: Dynein light chain roadblock-type 2 protein
+Macromolecule #8: Dynein light chain
+Macromolecule #9: Dynein light chain
+Macromolecule #10: Dynein light chain
+Macromolecule #11: Dynein light chain
+Macromolecule #12: Dynein light chain
+Macromolecule #13: Dynein light chain
+Macromolecule #14: Dynein light chain 2A
+Macromolecule #15: Dynein light chain tctex-type 1 protein
+Macromolecule #16: Thioredoxin
+Macromolecule #17: Tubulin beta chain
+Macromolecule #18: Tubulin alpha chain
+Macromolecule #19: Outer dynein arm docking complex protein oda protein
+Macromolecule #20: Docking complex 1/2 protein
+Macromolecule #21: Docking complex 1 protein
+Macromolecule #22: Outer dynein arm docking complex protein oda protein
+Macromolecule #23: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #24: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #25: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #26: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #27: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: C-flat-2/1 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force 3 for 5 seconds. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Average exposure time: 4.0 sec. / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 179 |
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Output model | PDB-7moq: |