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Yorodumi- EMDB-11576: Outer Dynein Arm-Shulin complex - overall structure (Tetrahymena ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11576 | |||||||||
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Title | Outer Dynein Arm-Shulin complex - overall structure (Tetrahymena thermophila) | |||||||||
Map data | Main map of overall ODA-Shulin structure (resampled on a full-length ODA-Shulin structure from a smaller subset of particles using EMDA). Unsharpened map. | |||||||||
Sample |
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Keywords | Cilia / dynein / microtubules / motor / MOTOR PROTEIN | |||||||||
Function / homology | Function and homology information outer dynein arm / axonemal dynein complex / outer dynein arm assembly / dynein light chain binding / cilium movement / dynein heavy chain binding / dynein complex / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding ...outer dynein arm / axonemal dynein complex / outer dynein arm assembly / dynein light chain binding / cilium movement / dynein heavy chain binding / dynein complex / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / motile cilium / dynein intermediate chain binding / microtubule-based movement / microtubule-based process / protein-disulfide reductase activity / microtubule / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Tetrahymena thermophila (strain SB210) (eukaryote) / Tetrahymena thermophila SB210 (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.78 Å | |||||||||
Authors | Mali GR / Abid Ali F / Lau CK / Carter AP | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Science / Year: 2021 Title: Shulin packages axonemal outer dynein arms for ciliary targeting. Authors: Girish R Mali / Ferdos Abid Ali / Clinton K Lau / Farida Begum / Jérôme Boulanger / Jonathan D Howe / Zhuo A Chen / Juri Rappsilber / Mark Skehel / Andrew P Carter / Abstract: The main force generators in eukaryotic cilia and flagella are axonemal outer dynein arms (ODAs). During ciliogenesis, these ~1.8-megadalton complexes are assembled in the cytoplasm and targeted to ...The main force generators in eukaryotic cilia and flagella are axonemal outer dynein arms (ODAs). During ciliogenesis, these ~1.8-megadalton complexes are assembled in the cytoplasm and targeted to cilia by an unknown mechanism. Here, we used the ciliate to identify two factors (Q22YU3 and Q22MS1) that bind ODAs in the cytoplasm and are required for ODA delivery to cilia. Q22YU3, which we named Shulin, locked the ODA motor domains into a closed conformation and inhibited motor activity. Cryo-electron microscopy revealed how Shulin stabilized this compact form of ODAs by binding to the dynein tails. Our findings provide a molecular explanation for how newly assembled dyneins are packaged for delivery to the cilia. | |||||||||
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_11576.map.gz | 323.3 MB | EMDB map data format | |
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Header (meta data) | emd-11576-v30.xml emd-11576.xml | 50.9 KB 50.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11576_fsc.xml | 27.5 KB | Display | FSC data file |
Images | emd_11576.png | 39.3 KB | ||
Masks | emd_11576_msk_1.map | 1.7 GB | Mask map | |
Filedesc metadata | emd-11576.cif.gz | 17.7 KB | ||
Others | emd_11576_half_map_1.map.gz emd_11576_half_map_2.map.gz | 478.6 MB 478.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11576 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11576 | HTTPS FTP |
-Validation report
Summary document | emd_11576_validation.pdf.gz | 165.3 KB | Display | EMDB validaton report |
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Full document | emd_11576_full_validation.pdf.gz | 165 KB | Display | |
Data in XML | emd_11576_validation.xml.gz | 500 B | Display | |
Data in CIF | emd_11576_validation.cif.gz | 375 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11576 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11576 | HTTPS FTP |
-Related structure data
Related structure data | 6zywMC 6zyxC 6zyyC 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_11576.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Main map of overall ODA-Shulin structure (resampled on a full-length ODA-Shulin structure from a smaller subset of particles using EMDA). Unsharpened map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11576_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map 2 of overall ODA-Shulin structure (Z-flipped, non-resampled)
File | emd_11576_half_map_1.map | ||||||||||||
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Annotation | Half map 2 of overall ODA-Shulin structure (Z-flipped, non-resampled) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 of overall ODA-Shulin structure (Z-flipped, non-resampled)
File | emd_11576_half_map_2.map | ||||||||||||
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Annotation | Half map 1 of overall ODA-Shulin structure (Z-flipped, non-resampled) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Tetrahymena thermophila ODA Dyh4 motor
+Supramolecule #1: Tetrahymena thermophila ODA Dyh4 motor
+Supramolecule #2: Tetrahymena thermophila ODA Dyh4 motor
+Supramolecule #3: Shulin
+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: Shulin
+Macromolecule #18: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #19: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #20: GUANOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R2/2 / Support film - Material: GRAPHENE OXIDE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-6zyw: |