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- EMDB-5621: Outer dynein arm - microtubule complex, biotin-streptavidin tagge... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5621 | |||||||||
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Title | Outer dynein arm - microtubule complex, biotin-streptavidin tagged at the carboxyl-terminus of the intermediate chain 2. | |||||||||
![]() | Outer dynein arm - microtubule complex, biotin-streptavidin tagged at the carboxyl-terminus of the intermediate chain 2. | |||||||||
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![]() | flagella / Chlamydomonas / outer dynein arm / microtubule / intermediate chain | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 34.0 Å | |||||||||
![]() | Oda T / Yagi T / Yanagisawa HA / Kikkawa M | |||||||||
![]() | ![]() Title: Identification of the outer-inner dynein linker as a hub controller for axonemal dynein activities. Authors: Toshiyuki Oda / Toshiki Yagi / Haruaki Yanagisawa / Masahide Kikkawa / ![]() Abstract: BACKGROUND: In flagella, the outer dynein arm (ODA) and inner dynein arm (IDA) play distinct roles in generating beating motion. However, functional communications between the two dyneins have not been investigated. RESULTS: Here, we demonstrated by cryo-electron microscopy and chemical crosslinking that intermediate chain 2 (IC2) of ODAs interacts with the dynein regulatory complex in the axoneme and ...RESULTS: Here, we demonstrated by cryo-electron microscopy and chemical crosslinking that intermediate chain 2 (IC2) of ODAs interacts with the dynein regulatory complex in the axoneme and constitutes part of the outer-inner dynein (OID) linker. Furthermore, we identified IC2 as a functional hub between ODAs and IDAs based on the phenotypes of Chlamydomonas mutants expressing biotinylation-tagged IC2. The flagella of the IC2 mutant showed activated microtubule sliding and enhanced ATPase activities of ODAs, as well as an altered waveform, indicating attenuated IDA activity. CONCLUSIONS: We concluded that the OID linker controls both ODAs and IDAs and regulates flagellar beating. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 8.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10 KB 10 KB | Display Display | ![]() |
Images | ![]() ![]() | 36.2 KB 2.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Outer dynein arm - microtubule complex, biotin-streptavidin tagged at the carboxyl-terminus of the intermediate chain 2. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.87 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Outer dynein arms from Chlamydomonas reinhardtii bound to porcine...
Entire | Name: Outer dynein arms from Chlamydomonas reinhardtii bound to porcine microtubules |
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Components |
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-Supramolecule #1000: Outer dynein arms from Chlamydomonas reinhardtii bound to porcine...
Supramolecule | Name: Outer dynein arms from Chlamydomonas reinhardtii bound to porcine microtubules type: sample / ID: 1000 Details: Streptavidin labels were attached to the biotinylation tag at the carboxyl-termini of IC2. Number unique components: 2 |
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-Supramolecule #1: Outer dynen arm-microbutule complex
Supramolecule | Name: Outer dynen arm-microbutule complex / type: organelle_or_cellular_component / ID: 1 Details: Streptavidin labels were attached to the biotinylation tag at the carboxyl-termini of IC2. Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | filament |
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Sample preparation
Concentration | 0.03 mg/mL |
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Buffer | pH: 7.4 Details: 10 mM Hepes-NaOH pH 7.4, 1 mM DTT, 5 mM MgCl2, 1 mM EGTA, 10% trehalose, 0.1% Nonidet P-40, 5 microM paclitaxel |
Grid | Details: 400 mesh copper grid with home-made holey carbon support, glow discharged in amylamine atmosphere |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 90 K / Instrument: LEICA KF80 Method: Two-side blot by hand for 10 seconds before plunging |
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Electron microscopy
Microscope | JEOL 2010F |
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Temperature | Min: 80 K / Max: 97 K / Average: 95 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 200,000 times magnification |
Date | May 5, 2011 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 10 µm / Number real images: 37 / Average electron dose: 7 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 40000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 3.3 mm / Nominal defocus max: 3.3 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 40000 |
Sample stage | Specimen holder: Gatan 626 Single Tilt Liquid Nitrogen Cryo Transfer Holder Specimen holder model: GATAN LIQUID NITROGEN |
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Image processing
CTF correction | Details: Wiener filter |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 122.3 Å Applied symmetry - Helical parameters - Δ&Phi: 179.2 ° Resolution.type: BY AUTHOR / Resolution: 34.0 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: FREALIGN / Number images used: 3024 |