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Yorodumi- EMDB-22679: Structure of outer-arm dynein bound to microtubule doublet in mic... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22679 | |||||||||
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Title | Structure of outer-arm dynein bound to microtubule doublet in microtubule binding state 2 (MTBS-2) | |||||||||
Map data | ||||||||||
Sample |
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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 / microtubule / calcium ion binding / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Tetrahymena thermophila (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Rao Q / Zhang K | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2021 Title: Structures of outer-arm dynein array on microtubule doublet reveal a motor coordination mechanism. Authors: Qinhui Rao / Long Han / Yue Wang / Pengxin Chai / Yin-Wei Kuo / Renbin Yang / Fangheng Hu / Yuchen Yang / Jonathon Howard / Kai Zhang / Abstract: Thousands of outer-arm dyneins (OADs) are arrayed in the axoneme to drive a rhythmic ciliary beat. Coordination among multiple OADs is essential for generating mechanical forces to bend microtubule ...Thousands of outer-arm dyneins (OADs) are arrayed in the axoneme to drive a rhythmic ciliary beat. Coordination among multiple OADs is essential for generating mechanical forces to bend microtubule doublets (MTDs). Using electron microscopy, we determined high-resolution structures of Tetrahymena thermophila OAD arrays bound to MTDs in two different states. OAD preferentially binds to MTD protofilaments with a pattern resembling the native tracks for its distinct microtubule-binding domains. Upon MTD binding, free OADs are induced to adopt a stable parallel conformation, primed for array formation. Extensive tail-to-head (TTH) interactions between OADs are observed, which need to be broken for ATP turnover by the dynein motor. We propose that OADs in an array sequentially hydrolyze ATP to slide the MTDs. ATP hydrolysis in turn relaxes the TTH interfaces to effect free nucleotide cycles of downstream OADs. These findings lead to a model explaining how conformational changes in the axoneme produce coordinated action of dyneins. | |||||||||
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_22679.map.gz | 8.7 MB | EMDB map data format | |
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Header (meta data) | emd-22679-v30.xml emd-22679.xml | 38.7 KB 38.7 KB | Display Display | EMDB header |
Images | emd_22679.png | 285.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22679 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22679 | HTTPS FTP |
-Validation report
Summary document | emd_22679_validation.pdf.gz | 333.4 KB | Display | EMDB validaton report |
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Full document | emd_22679_full_validation.pdf.gz | 332.9 KB | Display | |
Data in XML | emd_22679_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | emd_22679_validation.cif.gz | 4.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22679 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22679 | HTTPS FTP |
-Related structure data
Related structure data | 7k5bMC 7k58C 7kekC 7mwgC 7n32C C: citing same article (ref.) M: atomic model generated by this map |
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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_22679.map.gz / Format: CCP4 / Size: 193.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.333 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-arm dynein bound to microtubule doublet in microtubule bind...
+Supramolecule #1: Outer-arm dynein bound to microtubule doublet in microtubule bind...
+Macromolecule #1: Dynein heavy chain, outer arm protein
+Macromolecule #2: Outer arm dynein beta heavy chain
+Macromolecule #3: gamma heavy chain
+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 tctex-type 1 protein
+Macromolecule #15: Dynein light chain 2A
+Macromolecule #16: Thioredoxin
+Macromolecule #17: Dynein light chain 1
+Macromolecule #18: Dynein light chain 4A
+Macromolecule #19: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #20: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #21: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 53.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 76936 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |