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Yorodumi- PDB-6zyw: Outer Dynein Arm-Shulin complex - overall structure (Tetrahymena ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zyw | |||||||||
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Title | Outer Dynein Arm-Shulin complex - overall structure (Tetrahymena thermophila) | |||||||||
Components |
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Keywords | MOTOR PROTEIN / Cilia / dynein / microtubules / motor | |||||||||
Function / homology | Function and homology information outer dynein arm / axonemal dynein complex / outer dynein arm assembly / glycerol ether metabolic process / dynein light chain binding / cilium movement / dynein heavy chain binding / dynein complex / minus-end-directed microtubule motor activity / dynein light intermediate chain binding ...outer dynein arm / axonemal dynein complex / outer dynein arm assembly / glycerol ether metabolic process / dynein light chain binding / cilium movement / dynein heavy chain binding / 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 / cytoskeletal motor activity / microtubule-based process / protein-disulfide reductase activity / cell redox homeostasis / microtubule / centrosome / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Tetrahymena thermophila SB210 (eukaryote) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.78 Å | |||||||||
Authors | Mali, G.R. / Abid Ali, F. / Lau, C.K. / 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 | 6zyw.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6zyw.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 6zyw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zyw_validation.pdf.gz | 794.4 KB | Display | wwPDB validaton report |
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Full document | 6zyw_full_validation.pdf.gz | 823.7 KB | Display | |
Data in XML | 6zyw_validation.xml.gz | 205.9 KB | Display | |
Data in CIF | 6zyw_validation.cif.gz | 356.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/6zyw ftp://data.pdbj.org/pub/pdb/validation_reports/zy/6zyw | HTTPS FTP |
-Related structure data
Related structure data | 11576MC 6zyxC 6zyyC 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
-Protein , 6 types, 8 molecules ACDdEePY
#1: Protein | Mass: 475554.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7M6H4 | ||||||
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#3: Protein | Mass: 534328.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q22A67 | ||||||
#4: Protein | Mass: 77888.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7M008 #5: Protein | Mass: 77178.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q23FU1 #16: Protein | | Mass: 12855.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q240X9 #17: Protein | | Mass: 139935.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Shulin Source: (gene. exp.) Tetrahymena thermophila SB210 (eukaryote) Strain: SB210 / Gene: TTHERM_00122270 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q22YU3 |
-Dynein light ... , 10 types, 10 molecules FGHIJKLMNO
#6: Protein | Mass: 14751.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7MHB1 |
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#7: Protein | Mass: 11630.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q22MV2 |
#8: Protein | Mass: 10780.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: A4VE64 |
#9: Protein | Mass: 12348.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7MCM8 |
#10: Protein | Mass: 10973.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q24DI9 |
#11: Protein | Mass: 13336.089 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q22R86 |
#12: Protein | Mass: 12516.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: W7XJB1 |
#13: Protein | Mass: 10453.167 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q24CE5 |
#14: Protein | Mass: 15608.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q1HGH8 |
#15: Protein | Mass: 13202.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: A4VEB3 |
-Antibody , 1 types, 1 molecules B
#2: Antibody | Mass: 530182.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7M9J2 |
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-Non-polymers , 3 types, 5 molecules
#18: Chemical | #19: Chemical | ChemComp-ATP / | #20: Chemical | ChemComp-GTP / | |
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-Details
Has ligand of interest | N |
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-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 |
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Molecular weight | Value: 1.8 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) | ||||||||||||||||||||||||
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 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
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
3D reconstruction | Resolution: 8.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131142 / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT |