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Yorodumi- PDB-8tek: Baseplate of Nexin-dynein regulatory complex from Tetrahymena the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tek | |||||||||
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Title | Baseplate of Nexin-dynein regulatory complex from Tetrahymena thermophila | |||||||||
Components |
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Keywords | PROTEIN BINDING / complex / Cilia / axoneme / nexin-dynein regulatory complex | |||||||||
Function / homology | Function and homology information regulation of cilium movement / epithelial cilium movement involved in determination of left/right asymmetry / axonemal dynein complex assembly / inner dynein arm assembly / axonemal dynein complex / cilium-dependent cell motility / regulation of cilium beat frequency involved in ciliary motility / axoneme assembly / flagellated sperm motility / motile cilium ...regulation of cilium movement / epithelial cilium movement involved in determination of left/right asymmetry / axonemal dynein complex assembly / inner dynein arm assembly / axonemal dynein complex / cilium-dependent cell motility / regulation of cilium beat frequency involved in ciliary motility / axoneme assembly / flagellated sperm motility / motile cilium / positive regulation of cell motility / axoneme / cilium assembly / ciliary basal body / cell projection / cell motility / cilium / small GTPase binding / microtubule binding / microtubule / cytoskeleton / Golgi apparatus / extracellular region / cytoplasm Similarity search - Function | |||||||||
Biological species | Tetrahymena thermophila (eukaryote) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Ghanaeian, A.G. / Black, C.S. / Yang, S.K. / Bui, K.H. | |||||||||
Funding support | Canada, 2items
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Citation | Journal: Nat Commun / Year: 2023 Title: Integrated modeling of the Nexin-dynein regulatory complex reveals its regulatory mechanism. Authors: Avrin Ghanaeian / Sumita Majhi / Caitlyn L McCafferty / Babak Nami / Corbin S Black / Shun Kai Yang / Thibault Legal / Ophelia Papoulas / Martyna Janowska / Melissa Valente-Paterno / Edward ...Authors: Avrin Ghanaeian / Sumita Majhi / Caitlyn L McCafferty / Babak Nami / Corbin S Black / Shun Kai Yang / Thibault Legal / Ophelia Papoulas / Martyna Janowska / Melissa Valente-Paterno / Edward M Marcotte / Dorota Wloga / Khanh Huy Bui / Abstract: Cilia are hairlike protrusions that project from the surface of eukaryotic cells and play key roles in cell signaling and motility. Ciliary motility is regulated by the conserved nexin-dynein ...Cilia are hairlike protrusions that project from the surface of eukaryotic cells and play key roles in cell signaling and motility. Ciliary motility is regulated by the conserved nexin-dynein regulatory complex (N-DRC), which links adjacent doublet microtubules and regulates and coordinates the activity of outer doublet complexes. Despite its critical role in cilia motility, the assembly and molecular basis of the regulatory mechanism are poorly understood. Here, using cryo-electron microscopy in conjunction with biochemical cross-linking and integrative modeling, we localize 12 DRC subunits in the N-DRC structure of Tetrahymena thermophila. We also find that the CCDC96/113 complex is in close contact with the DRC9/10 in the linker region. In addition, we reveal that the N-DRC is associated with a network of coiled-coil proteins that most likely mediates N-DRC regulatory activity. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tek.cif.gz | 426.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tek.ent.gz | 294.1 KB | Display | PDB format |
PDBx/mmJSON format | 8tek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tek_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8tek_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8tek_validation.xml.gz | 72.3 KB | Display | |
Data in CIF | 8tek_validation.cif.gz | 106.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/8tek ftp://data.pdbj.org/pub/pdb/validation_reports/te/8tek | HTTPS FTP |
-Related structure data
Related structure data | 41189MC 8th8C 8tidC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 6 types, 6 molecules AMNPTg
#1: Protein | Mass: 98840.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: The baseplate domain of the DRC1 / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q229S1 |
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#5: Protein | Mass: 76154.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7LWP7 |
#6: Protein | Mass: 114163.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q23BW0 |
#8: Protein | Mass: 94540.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7M6D6 |
#9: Protein | Mass: 42931.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22KK0 |
#10: Protein | Mass: 22976.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22NU3 |
-Coiled-coil protein, ... , 2 types, 2 molecules BO
#2: Protein | Mass: 60596.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: The baseplate domain of the DRC2 / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q24DJ0 |
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#7: Protein | Mass: 105196.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q233L0 |
-Growth-arrest-specific microtubule-binding ... , 2 types, 2 molecules DE
#3: Protein | Mass: 56190.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7LT80 |
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#4: Protein | Mass: 55393.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q23YW7 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: CELL / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Baseplate of Nexin-dynein regulatory complex from Tetrahymena thermophila Type: ORGANELLE OR CELLULAR COMPONENT Details: Single Particle Analysis of baseplate domain of Nexin-Dynein regulatory complex of Tetrahymena thermophila Entity ID: #8-#9, #1-#7, #10 / Source: NATURAL |
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Source (natural) | Organism: Tetrahymena thermophila (eukaryote) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.6 Å / Resolution method: OTHER / Num. of particles: 211502 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.78 Å2 | ||||||||||||||||||||||||
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