|Entry||Database: EMDB / ID: 3787|
|Title||Cryo-electron tomography averaged map of microtubule doublet from p23 mutant Chlamydomonas axoneme|
|Map data||Subaverage after subtomogram classification of Chlamydomonas pf23 cilia, based on outer arm dynein structure.|
|Sample||Ciliary microtubule doublet with dynein, radial spokes and other binding proteins:|
|Source||Chlamydomonas reinhardtii (plant)|
|Method||subtomogram averaging / cryo EM / 50 Å resolution|
|Authors||Sale WS / Ishikawa T / Yamamoto R / Obbineni JM / Alford LM / Hwang J / Ide T / Owa M / Kon T / Inaba K / Noliyanda J / King SM / Dutcher S|
|Citation||Journal: PLoS Genet. / Year: 2017|
Title: Chlamydomonas DYX1C1/PF23 is essential for axonemal assembly and proper morphology of inner dynein arms.
Authors: Ryosuke Yamamoto / Jagan M Obbineni / Lea M Alford / Takahiro Ide / Mikito Owa / Juyeon Hwang / Takahide Kon / Kazuo Inaba / Noliyanda James / Stephen M King / Takashi Ishikawa / Winfield S Sale / Susan K Dutcher
Abstract: Cytoplasmic assembly of ciliary dyneins, a process known as preassembly, requires numerous non-dynein proteins, but the identities and functions of these proteins are not fully elucidated. Here, we ...Cytoplasmic assembly of ciliary dyneins, a process known as preassembly, requires numerous non-dynein proteins, but the identities and functions of these proteins are not fully elucidated. Here, we show that the classical Chlamydomonas motility mutant pf23 is defective in the Chlamydomonas homolog of DYX1C1. The pf23 mutant has a 494 bp deletion in the DYX1C1 gene and expresses a shorter DYX1C1 protein in the cytoplasm. Structural analyses, using cryo-ET, reveal that pf23 axonemes lack most of the inner dynein arms. Spectral counting confirms that DYX1C1 is essential for the assembly of the majority of ciliary inner dynein arms (IDA) as well as a fraction of the outer dynein arms (ODA). A C-terminal truncation of DYX1C1 shows a reduction in a subset of these ciliary IDAs. Sucrose gradients of cytoplasmic extracts show that preassembled ciliary dyneins are reduced compared to wild-type, which suggests an important role in dynein complex stability. The role of PF23/DYX1C1 remains unknown, but we suggest that DYX1C1 could provide a scaffold for macromolecular assembly.
|Date||Deposition: Jul 6, 2017 / Header (metadata) release: Aug 16, 2017 / Map release: Sep 6, 2017 / Last update: Sep 20, 2017|
|Structure viewer||EM map: |
Downloads & links
|File||emd_3787.map.gz (map file in CCP4 format, 49949 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 5.68 Å|
CCP4 map header:
-Entire Ciliary microtubule doublet with dynein, radial spokes and other ...
|Entire||Name: Ciliary microtubule doublet with dynein, radial spokes and other binding proteins|
Number of components: 1
-Component #1: cellular-component, Ciliary microtubule doublet with dynein, radi...
|Cellular-component||Name: Ciliary microtubule doublet with dynein, radial spokes and other binding proteins|
Recombinant expression: No
|Source||Species: Chlamydomonas reinhardtii (plant) / Strain: pf23|
|Source (natural)||Organelle: cilia|
|Specimen||Specimen state: cell / Method: cryo EM|
|Sample solution||Buffer solution: 30 mM HEPES, 5 mM MgSO4, 1 mM DTT, 1 mM EGTA, and 50 mM potassium acetate, pH7.4|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 70 % / Details: one side blotting|
-Electron microscopy imaging
|Imaging||Microscope: JEOL 2200FS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 0.8 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 20000 X (nominal) / Imaging mode: BRIGHT FIELD / Energy filter: JEOL in-column / Energy window: 0-25 eV|
|Specimen Holder||Model: GATAN LIQUID NITROGEN / Tilt Angle: -60 - 60 deg.|
|Camera||Detector: TVIPS TEMCAM-F416 (4k x 4k)|
|Processing||Method: subtomogram averaging|
|3D reconstruction||Algorithm: BACK PROJECTION / Software: SPIDER / Resolution: 50 Å / Resolution method: OTHER|
Details: Visual estimation, compared with datasets in the past
Euler angles: 3D cross correlation by Spider
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
-Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
+Apr 13, 2016. Omokage search got faster
Omokage search got faster
- The computation time became ~1/2 compared to the previous version by re-optimization of data accession
- Enjoy "shape similarity" of biomolecules, more!
Related info.: Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- All the functionalities will be ported from the levgacy version.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi