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Yorodumi- EMDB-1696: Outer Dynein arms with a Microtubule Doublet in the absence of nu... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1696 | |||||||||
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Title | Outer Dynein arms with a Microtubule Doublet in the absence of nucleotides | |||||||||
Map data | This is an image of outer dynein arms on a microtubule doublet in flagella | |||||||||
Sample |
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Keywords | Dynein / flagella / tubulin / microtubule / motility | |||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 37.0 Å | |||||||||
Authors | Movassagh T / Bui KH / Sakakibara H / Oiwa K / Ishikawa T | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2010 Title: Nucleotide-induced global conformational changes of flagellar dynein arms revealed by in situ analysis. Authors: Tandis Movassagh / Khanh Huy Bui / Hitoshi Sakakibara / Kazuhiro Oiwa / Takashi Ishikawa / Abstract: Outer and inner dynein arms generate force for the flagellar/ciliary bending motion. Although nucleotide-induced structural change of dynein heavy chains (the ATP-driven motor) was proven in vitro, ...Outer and inner dynein arms generate force for the flagellar/ciliary bending motion. Although nucleotide-induced structural change of dynein heavy chains (the ATP-driven motor) was proven in vitro, our lack of knowledge in situ has precluded an understanding of the bending mechanism. Here we reveal nucleotide-induced global structural changes of the outer and inner dynein arms of Chlamydomonas reinhardtii flagella in situ using electron cryotomography. The ATPase domains of the dynein heavy chains move toward the distal end, and the N-terminal tail bends sharply during product release. This motion could drive the adjacent microtubule to cause a sliding motion. In contrast to in vitro results, in the presence of nucleotides, outer dynein arms coexist as clusters of apo or nucleotide-bound forms in situ. This implies a cooperative switching, which may be related to the mechanism of bending. | |||||||||
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_1696.map.gz | 2.8 MB | EMDB map data format | |
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Header (meta data) | emd-1696-v30.xml emd-1696.xml | 9.3 KB 9.3 KB | Display Display | EMDB header |
Images | 1696apo.jpg | 72.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1696 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1696 | HTTPS FTP |
-Validation report
Summary document | emd_1696_validation.pdf.gz | 181.3 KB | Display | EMDB validaton report |
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Full document | emd_1696_full_validation.pdf.gz | 180.4 KB | Display | |
Data in XML | emd_1696_validation.xml.gz | 4.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1696 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1696 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1696.map.gz / Format: CCP4 / Size: 3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is an image of outer dynein arms on a microtubule doublet in flagella | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.85 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 : Outer dynein arm, microtubule doublet
Entire | Name: Outer dynein arm, microtubule doublet |
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Components |
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-Supramolecule #1000: Outer dynein arm, microtubule doublet
Supramolecule | Name: Outer dynein arm, microtubule doublet / type: sample / ID: 1000 / Details: The sample was flagella in situ Oligomeric state: One heterotrimer binds to one microtubule doublet Number unique components: 1 |
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-Supramolecule #1: Flagella
Supramolecule | Name: Flagella / type: organelle_or_cellular_component / ID: 1 / Name.synonym: Outer dynein arm and Microtubule doublet / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) / synonym: Green algae / Cell: Chlamydomonas reinhardtii / Organelle: Flagella / Location in cell: Axoneme |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Details: 30 mM HEPES (pH 7.4), 5 mM MgSO4, 1 mM DTT, 1 mM EGTA, 50 mM Potassium Acetate, 0.5% (w/v) Polyethylene Glycol (MW 20,000) |
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Grid | Details: 300 mesh lacey carbon grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 3 seconds before plunging |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 100 K |
Specialist optics | Energy filter - Name: GIF / Energy filter - Lower energy threshold: 10.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Image recording | Category: CCD / Film or detector model: GENERIC GATAN / Digitization - Sampling interval: 6.85 µm / Number real images: 1200 / Average electron dose: 30 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | Average number of projections used in the 3D reconstructions: 6000. Average number of class averages: 1. |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 37.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD |