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Yorodumi- PDB-6zyy: Outer Dynein Arm-Shulin complex - Dyh3 motor region (Tetrahymena ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zyy | |||||||||
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Title | Outer Dynein Arm-Shulin complex - Dyh3 motor region (Tetrahymena thermophila) | |||||||||
Components |
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Keywords | MOTOR PROTEIN / Cilia / dynein / microtubules / motor | |||||||||
Function / homology | Function and homology information axonemal dynein complex / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / dynein intermediate chain binding / microtubule-based movement / microtubule / ATP hydrolysis activity / ATP binding Similarity search - Function | |||||||||
Biological species | Tetrahymena thermophila (eukaryote) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | Mali, G.R. / Abid Ali, F. / Lau, C.K. / Begum, F. / Boulanger, J. / Howe, J.D. / Chen, Z.A. / Rappsilber, J. / Skehel, M. / Carter, A.P. | |||||||||
Funding support | United Kingdom, 2items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6zyy.cif.gz | 578.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zyy.ent.gz | 426 KB | Display | PDB format |
PDBx/mmJSON format | 6zyy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zyy_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6zyy_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6zyy_validation.xml.gz | 95.3 KB | Display | |
Data in CIF | 6zyy_validation.cif.gz | 142.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/6zyy ftp://data.pdbj.org/pub/pdb/validation_reports/zy/6zyy | HTTPS FTP |
-Related structure data
Related structure data | 11581MC 6zywC 6zyxC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 534328.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Tetrahymena thermophila (strain SB210) (eukaryote) Strain: SB210 / References: UniProt: Q22A67 | ||||
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#2: Protein | Mass: 139935.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tetrahymena thermophila (strain SB210) (eukaryote) Strain: SB210 / Gene: TTHERM_00122270 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q22YU3 | ||||
#3: Chemical | #4: Chemical | ChemComp-ATP / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Tetrahymena thermophila ODA Dyh3 motor region (includes Shulin C3 finger) Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL |
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Molecular weight | Value: 1.8 MDa / Experimental value: NO |
Source (natural) | Organism: Tetrahymena thermophila (eukaryote) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: dev_3965: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49397 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||
Refine LS restraints |
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