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Yorodumi- EMDB-41284: Combined linker domain of N-DRC and associated proteins Tetrahymena -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41284 | |||||||||
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Title | Combined linker domain of N-DRC and associated proteins Tetrahymena | |||||||||
Map data | Main map | |||||||||
Sample |
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Keywords | nexin-dynein regulatory complex / cilia / axoneme / dynein / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information regulation of cilium movement / axonemal dynein complex assembly / axonemal dynein complex / inner dynein arm assembly / cilium-dependent cell motility / regulation of cilium beat frequency involved in ciliary motility / cilium movement / axoneme assembly / regulation of Arp2/3 complex-mediated actin nucleation / cilium organization ...regulation of cilium movement / axonemal dynein complex assembly / axonemal dynein complex / inner dynein arm assembly / cilium-dependent cell motility / regulation of cilium beat frequency involved in ciliary motility / cilium movement / axoneme assembly / regulation of Arp2/3 complex-mediated actin nucleation / cilium organization / motile cilium / positive regulation of cell motility / axoneme / cilium assembly / ciliary basal body / cell projection / cell motility / cilium / small GTPase binding / cell migration / lamellipodium / microtubule binding / microtubule / cytoskeleton / calcium ion binding / Golgi apparatus / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Tetrahymena thermophila (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Ghanaeian AG / Majhi SM / McCaffrey CM / Nami BN / Black CB / Yang SK / Legal TL / Papoulas OP / Janowska MJ / Valente-Paterno MV ...Ghanaeian AG / Majhi SM / McCaffrey CM / Nami BN / Black CB / Yang SK / Legal TL / Papoulas OP / Janowska MJ / Valente-Paterno MV / Marcotte EM / Wloga DW / Bui KH | |||||||||
Funding support | Canada, 2 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41284.map.gz | 369.7 MB | EMDB map data format | |
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Header (meta data) | emd-41284-v30.xml emd-41284.xml | 51.2 KB 51.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41284_fsc.xml | 15.4 KB | Display | FSC data file |
Images | emd_41284.png | 95.7 KB | ||
Masks | emd_41284_msk_1.map | 396.1 MB | Mask map | |
Filedesc metadata | emd-41284.cif.gz | 15.6 KB | ||
Others | emd_41284_half_map_1.map.gz emd_41284_half_map_2.map.gz | 367.4 MB 367.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41284 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41284 | HTTPS FTP |
-Validation report
Summary document | emd_41284_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_41284_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_41284_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | emd_41284_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41284 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41284 | HTTPS FTP |
-Related structure data
Related structure data | 8tidMC 8tekC 8th8C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41284.map.gz / Format: CCP4 / Size: 401.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Main map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.74 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_41284_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map
File | emd_41284_half_map_1.map | ||||||||||||
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Annotation | Half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map
File | emd_41284_half_map_2.map | ||||||||||||
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Annotation | Half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Combined linker domain of N-DRC and associated proteins Tetrahymena
+Supramolecule #1: Combined linker domain of N-DRC and associated proteins Tetrahymena
+Macromolecule #1: Dynein regulatory complex protein 1/2 N-terminal domain-containin...
+Macromolecule #2: Coiled-coil protein, putative
+Macromolecule #3: LRRC48 protein
+Macromolecule #4: Growth-arrest-specific microtubule-binding protein
+Macromolecule #5: Growth-arrest-specific microtubule-binding protein
+Macromolecule #6: Flagellar associated protein
+Macromolecule #7: Kinase domain protein
+Macromolecule #8: Coiled-coil lobo-like protein, putative
+Macromolecule #9: EF-hand calcium-binding domain protein
+Macromolecule #10: Dynein regulatory complex protein 9
+Macromolecule #11: Dynein regulatory complex protein 10
+Macromolecule #12: AAA family ATPase CDC48 subfamily protein
+Macromolecule #13: Cilia- and flagella-associated protein 91
+Macromolecule #14: Flagella associated protein
+Macromolecule #15: Coiled-coil protein, putative
+Macromolecule #16: DUF4201 domain-containing protein
+Macromolecule #17: Calmodulin 7-2
+Macromolecule #18: Coiled-coil domain-containing protein 153
+Macromolecule #19: Flagellar associated protein
+Macromolecule #20: L-shape (Unknown-protein)
+Macromolecule #21: WD40 domain protein
+Macromolecule #22: EF hand protein
+Macromolecule #23: CFAP20
+Macromolecule #24: WD40 domain protein
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | cell |
-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 K3 (6k x 4k) / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |