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Yorodumi- EMDB-23082: Outer dynein arm bound to doublet microtubules from C. reinhardtii -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23082 | |||||||||
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Title | Outer dynein arm bound to doublet microtubules from C. reinhardtii | |||||||||
Map data | Composite map of the complete ODA complex bound to doublet microtubules | |||||||||
Sample |
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Keywords | dynein / microtubule / cilia / MOTOR PROTEIN | |||||||||
Function / homology | Function and homology information outer dynein arm / outer dynein arm assembly / cilium movement involved in cell motility / 9+2 motile cilium / dynein light chain binding / cilium movement / motile cilium assembly / dynein heavy chain binding / cell projection organization / dynein complex ...outer dynein arm / outer dynein arm assembly / cilium movement involved in cell motility / 9+2 motile cilium / dynein light chain binding / cilium movement / motile cilium assembly / dynein heavy chain binding / cell projection organization / dynein complex / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / ciliary plasm / motile cilium / dynein intermediate chain binding / microtubule-based movement / axoneme / microtubule-based process / enzyme regulator activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / microtubule / hydrolase activity / GTPase activity / calcium ion binding / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 7.5 Å | |||||||||
Authors | Walton T / Wu H | |||||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Structure of a microtubule-bound axonemal dynein. Authors: Travis Walton / Hao Wu / Alan Brown / Abstract: Axonemal dyneins are tethered to doublet microtubules inside cilia to drive ciliary beating, a process critical for cellular motility and extracellular fluid flow. Axonemal dyneins are evolutionarily ...Axonemal dyneins are tethered to doublet microtubules inside cilia to drive ciliary beating, a process critical for cellular motility and extracellular fluid flow. Axonemal dyneins are evolutionarily and biochemically distinct from cytoplasmic dyneins that transport cargo, and the mechanisms regulating their localization and function are poorly understood. Here, we report a single-particle cryo-EM reconstruction of a three-headed axonemal dynein natively bound to doublet microtubules isolated from cilia. The slanted conformation of the axonemal dynein causes interaction of its motor domains with the neighboring dynein complex. Our structure shows how a heterotrimeric docking complex specifically localizes the linear array of axonemal dyneins to the doublet microtubule by directly interacting with the heavy chains. Our structural analysis establishes the arrangement of conserved heavy, intermediate and light chain subunits, and provides a framework to understand the roles of individual subunits and the interactions between dyneins during ciliary waveform generation. | |||||||||
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_23082.map.gz | 18.8 MB | EMDB map data format | |
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Header (meta data) | emd-23082-v30.xml emd-23082.xml | 66.1 KB 66.1 KB | Display Display | EMDB header |
Images | emd_23082.png | 95.7 KB | ||
Filedesc metadata | emd-23082.cif.gz | 19 KB | ||
Others | emd_23082_additional_1.map.gz emd_23082_additional_2.map.gz emd_23082_additional_3.map.gz emd_23082_additional_4.map.gz emd_23082_additional_5.map.gz emd_23082_additional_6.map.gz emd_23082_additional_7.map.gz emd_23082_additional_8.map.gz | 1.1 GB 1.1 GB 163.3 MB 3.2 MB 2.8 MB 7.1 MB 3.6 MB 6.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23082 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23082 | HTTPS FTP |
-Related structure data
Related structure data | 7kzmMC 7kznC 7kzoC 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_23082.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Composite map of the complete ODA complex bound to doublet microtubules | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Half map 2 for full ODA map containing two adjacent complexes.
File | emd_23082_additional_1.map | ||||||||||||
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Annotation | Half map 2 for full ODA map containing two adjacent complexes. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Half map 1 for full ODA map containing two adjacent complexes.
File | emd_23082_additional_2.map | ||||||||||||
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Annotation | Half map 1 for full ODA map containing two adjacent complexes. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Full ODA map containing two adjacent complexes.
File | emd_23082_additional_3.map | ||||||||||||
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Annotation | Full ODA map containing two adjacent complexes. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map of heavy chain beta AAA motor domain, class 1.
File | emd_23082_additional_4.map | ||||||||||||
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Annotation | Map of heavy chain beta AAA motor domain, class 1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map of heavy chain gamma AAA motor domain.
File | emd_23082_additional_5.map | ||||||||||||
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Annotation | Map of heavy chain gamma AAA motor domain. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map of heavy chain alpha tail region.
File | emd_23082_additional_6.map | ||||||||||||
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Annotation | Map of heavy chain alpha tail region. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map of heavy chain alpha AAA motor domain.
File | emd_23082_additional_7.map | ||||||||||||
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Annotation | Map of heavy chain alpha AAA motor domain. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map of heavy chain beta AAA motor domain, class 2.
File | emd_23082_additional_8.map | ||||||||||||
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Annotation | Map of heavy chain beta AAA motor domain, class 2. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : ODA complex
+Supramolecule #1: ODA complex
+Macromolecule #1: Tubulin beta
+Macromolecule #2: Tubulin alpha
+Macromolecule #3: Heavy chain alpha
+Macromolecule #4: Flagellar outer dynein arm heavy chain beta
+Macromolecule #5: Dynein gamma chain, flagellar outer arm
+Macromolecule #6: Dynein, 78 kDa intermediate chain, flagellar outer arm
+Macromolecule #7: Dynein, 70 kDa intermediate chain, flagellar outer arm
+Macromolecule #8: Flagellar outer dynein arm light chain 2
+Macromolecule #9: Dynein 18 kDa light chain, flagellar outer arm
+Macromolecule #10: Dynein 11 kDa light chain, flagellar outer arm
+Macromolecule #11: Dynein light chain roadblock LC7a
+Macromolecule #12: Dynein light chain roadblock LC7b
+Macromolecule #13: Dynein 8 kDa light chain, flagellar outer arm
+Macromolecule #14: Dynein light chain 9
+Macromolecule #15: Dynein light chain 10
+Macromolecule #16: Outer dynein arm-docking complex subunit 1
+Macromolecule #17: DC1
+Macromolecule #18: Outer dynein arm protein 1
+Macromolecule #19: DC2
+Macromolecule #20: Outer dynein arm-docking complex protein DC3
+Macromolecule #21: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #22: MAGNESIUM ION
+Macromolecule #23: GUANOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 20 mg/mL | |||||||||||||||||||||
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Buffer | pH: 7.4 Component:
Details: Buffer also contained 1x Protease Arrest (G-Biosciences) | |||||||||||||||||||||
Grid | Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 15 mA | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV Details: 2.5 ul of splayed axoneme solution was then dispensed onto glow-discharged C-Flat 1.2/1.3-4Cu grids inside a Vitrobot Mark IV under 100% humidity. After a 10 s delay time, cryo-EM samples ...Details: 2.5 ul of splayed axoneme solution was then dispensed onto glow-discharged C-Flat 1.2/1.3-4Cu grids inside a Vitrobot Mark IV under 100% humidity. After a 10 s delay time, cryo-EM samples were prepared by first blotting for 10 s with blot force set to 16 and immediately plunged into liquid ethane.. | |||||||||||||||||||||
Details | Splayed axonemes isolated from Chlamydomonas reinhardtii flagella. |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 25 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 20524 / Average exposure time: 3.7 sec. / Average electron dose: 61.48 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Segment selection | Number selected: 5584147 / Software - Name: RELION (ver. 3.1) |
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Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: RELION (ver. 3.1) |
Final reconstruction | Applied symmetry - Helical parameters - Δz: 82.0 Å Applied symmetry - Helical parameters - Δ&Phi: 0 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) Details: The composite map varies in resolution from 3.5 to 12 A. The reference map is 7.5 A. Number images used: 485694 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER / Target criteria: Correlation coefficient |
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Output model | PDB-7kzm: |