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Yorodumi- EMDB-29667: 96-nm repeat unit of intact doublet microtubule from Tetrahymena ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29667 | |||||||||
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Title | 96-nm repeat unit of intact doublet microtubule from Tetrahymena thermophila strain CU428 | |||||||||
Map data | CU428 96 nm subtomogram average postprocess | |||||||||
Sample |
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Keywords | Cilia / Axoneme / Doublet Microtubule / Microtubule Inner Protein / STRUCTURAL PROTEIN | |||||||||
Biological species | Tetrahymena thermophila (eukaryote) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 19.0 Å | |||||||||
Authors | Black CS / Legal T / Bui KH | |||||||||
Funding support | Canada, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Native doublet microtubules from Tetrahymena thermophila reveal the importance of outer junction proteins. Authors: Shintaroh Kubo / Corbin S Black / Ewa Joachimiak / Shun Kai Yang / Thibault Legal / Katya Peri / Ahmad Abdelzaher Zaki Khalifa / Avrin Ghanaeian / Caitlyn L McCafferty / Melissa Valente- ...Authors: Shintaroh Kubo / Corbin S Black / Ewa Joachimiak / Shun Kai Yang / Thibault Legal / Katya Peri / Ahmad Abdelzaher Zaki Khalifa / Avrin Ghanaeian / Caitlyn L McCafferty / Melissa Valente-Paterno / Chelsea De Bellis / Phuong M Huynh / Zhe Fan / Edward M Marcotte / Dorota Wloga / Khanh Huy Bui / Abstract: Cilia are ubiquitous eukaryotic organelles responsible for cellular motility and sensory functions. The ciliary axoneme is a microtubule-based cytoskeleton consisting of two central singlets and nine ...Cilia are ubiquitous eukaryotic organelles responsible for cellular motility and sensory functions. The ciliary axoneme is a microtubule-based cytoskeleton consisting of two central singlets and nine outer doublet microtubules. Cryo-electron microscopy-based studies have revealed a complex network inside the lumen of both tubules composed of microtubule-inner proteins (MIPs). However, the functions of most MIPs remain unknown. Here, we present single-particle cryo-EM-based analyses of the Tetrahymena thermophila native doublet microtubule and identify 42 MIPs. These data shed light on the evolutionarily conserved and diversified roles of MIPs. In addition, we identified MIPs potentially responsible for the assembly and stability of the doublet outer junction. Knockout of the evolutionarily conserved outer junction component CFAP77 moderately diminishes Tetrahymena swimming speed and beat frequency, indicating the important role of CFAP77 and outer junction stability in cilia beating generation and/or regulation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29667.map.gz | 11.9 MB | EMDB map data format | |
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Header (meta data) | emd-29667-v30.xml emd-29667.xml | 13 KB 13 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29667_fsc.xml | 6.1 KB | Display | FSC data file |
Images | emd_29667.png | 82.5 KB | ||
Others | emd_29667_half_map_1.map.gz emd_29667_half_map_2.map.gz | 13.8 MB 13.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29667 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29667 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_29667.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | CU428 96 nm subtomogram average postprocess | ||||||||||||||||||||
Voxel size | X=Y=Z: 8.48 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: CU428 96 nm subtomogram average half map 1
File | emd_29667_half_map_1.map | ||||||||||||
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Annotation | CU428 96 nm subtomogram average half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: CU428 96 nm subtomogram average half map 2
File | emd_29667_half_map_2.map | ||||||||||||
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Annotation | CU428 96 nm subtomogram average half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 96-nm repeat unit of microtubule doublet from Tetrahymena thermophila
Entire | Name: 96-nm repeat unit of microtubule doublet from Tetrahymena thermophila |
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Components |
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-Supramolecule #1: 96-nm repeat unit of microtubule doublet from Tetrahymena thermophila
Supramolecule | Name: 96-nm repeat unit of microtubule doublet from Tetrahymena thermophila type: organelle_or_cellular_component / ID: 1 / Parent: 0 Details: Subtomogram average of the 96-nm repeating unit of the axoneme from intact cilia purified from CFAP77AB-KO mutant |
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Source (natural) | Organism: Tetrahymena thermophila (eukaryote) / Strain: CFAP77AB-KO / Organelle: Cilia |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Concentration | 1.8 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.5 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 4.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |