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Yorodumi- EMDB-6164: Detailed Structural and biochemical characterization of the nexin... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6164 | |||||||||
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Title | Detailed Structural and biochemical characterization of the nexin-dynein regulatory complex | |||||||||
Map data | Streptavidin-labeled N-DRC structure from DRC5-C-BCCP axoneme | |||||||||
Sample |
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Keywords | cilia and flagella / axoneme / dynein regulatory complex | |||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 45.0 Å | |||||||||
Authors | Oda T / Yanagisawa H / Kikkawa M | |||||||||
Citation | Journal: Mol Biol Cell / Year: 2015 Title: Detailed structural and biochemical characterization of the nexin-dynein regulatory complex. Authors: Toshiyuki Oda / Haruaki Yanagisawa / Masahide Kikkawa / Abstract: The nexin-dynein regulatory complex (N-DRC) forms a cross-bridge between the outer doublet microtubules of the axoneme and regulates dynein motor activity in cilia/flagella. Although the molecular ...The nexin-dynein regulatory complex (N-DRC) forms a cross-bridge between the outer doublet microtubules of the axoneme and regulates dynein motor activity in cilia/flagella. Although the molecular composition and the three-dimensional structure of N-DRC have been studied using mutant strains lacking N-DRC subunits, more accurate approaches are necessary to characterize the structure and function of N-DRC. In this study, we precisely localized DRC1, DRC2, and DRC4 using cryo-electron tomography and structural labeling. All three N-DRC subunits had elongated conformations and spanned the length of N-DRC. Furthermore, we purified N-DRC and characterized its microtubule-binding properties. Purified N-DRC bound to the microtubule and partially inhibited microtubule sliding driven by the outer dynein arms (ODAs). Of interest, microtubule sliding was observed even in the presence of fourfold molar excess of N-DRC relative to ODA. These results provide insights into the role of N-DRC in generating the beating motions of cilia/flagella. | |||||||||
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_6164.map.gz | 2.7 MB | EMDB map data format | |
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Header (meta data) | emd-6164-v30.xml emd-6164.xml | 8.6 KB 8.6 KB | Display Display | EMDB header |
Images | 400_6164.gif 80_6164.gif | 37.4 KB 3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6164 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6164 | HTTPS FTP |
-Validation report
Summary document | emd_6164_validation.pdf.gz | 77.8 KB | Display | EMDB validaton report |
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Full document | emd_6164_full_validation.pdf.gz | 76.9 KB | Display | |
Data in XML | emd_6164_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6164 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6164 | HTTPS FTP |
-Related structure data
Related structure data | 6154C 6155C 6156C 6157C 6158C 6159C 6160C 6161C 6162C 6163C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6164.map.gz / Format: CCP4 / Size: 3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Streptavidin-labeled N-DRC structure from DRC5-C-BCCP axoneme | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.07 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 : Streptavidin-labeled N-DRC structure from DRC5-C-BCCP axoneme
Entire | Name: Streptavidin-labeled N-DRC structure from DRC5-C-BCCP axoneme |
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Components |
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-Supramolecule #1000: Streptavidin-labeled N-DRC structure from DRC5-C-BCCP axoneme
Supramolecule | Name: Streptavidin-labeled N-DRC structure from DRC5-C-BCCP axoneme type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: axoneme
Supramolecule | Name: axoneme / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) / Organelle: flagella |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Concentration | 0.01 mg/mL |
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Buffer | pH: 7.2 Details: 30 mM Hepes-NaOH pH 7.2, 5 mM MgCl2, 1 mM dithiothreitol, 1 mM EGTA, 50 mM NaCl |
Grid | Details: 300 mesh copper grid, holey carbon |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 93 K / Instrument: LEICA EM GP / Method: Blot for 5 seconds before plunging |
-Electron microscopy
Microscope | JEOL 3100FFC |
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Specialist optics | Energy filter - Name: Omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Date | Jan 3, 2014 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 100 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 7.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 25700 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -65 ° / Tilt series - Axis1 - Max angle: 65 ° |
-Image processing
Details | Number of tilts (projections) used in 3D reconstruction: 65 Tomographic tilt angle increment: 2 |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 45.0 Å / Resolution method: OTHER / Software - Name: IMOD, PEET |