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Yorodumi- EMDB-40896: Tip central pair consensus map from Tetrahymena thermophila cilia -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40896 | |||||||||
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Title | Tip central pair consensus map from Tetrahymena thermophila cilia | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Cilia / Axoneme / central pair / microtubules / STRUCTURAL PROTEIN | |||||||||
Biological species | Tetrahymena thermophila (eukaryote) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 12.6 Å | |||||||||
Authors | Legal T / Bui KH | |||||||||
Funding support | Canada, 1 items
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Citation | Journal: J Cell Biol / Year: 2023 Title: CEP104/FAP256 and associated cap complex maintain stability of the ciliary tip. Authors: Thibault Legal / Mireya Parra / Maxwell Tong / Corbin S Black / Ewa Joachimiak / Melissa Valente-Paterno / Karl Lechtreck / Jacek Gaertig / Khanh Huy Bui / Abstract: Cilia are essential organelles that protrude from the cell body. Cilia are made of a microtubule-based structure called the axoneme. In most types of cilia, the ciliary tip is distinct from the rest ...Cilia are essential organelles that protrude from the cell body. Cilia are made of a microtubule-based structure called the axoneme. In most types of cilia, the ciliary tip is distinct from the rest of the cilium. Here, we used cryo-electron tomography and subtomogram averaging to obtain the structure of the ciliary tip of the ciliate Tetrahymena thermophila. We show that the microtubules at the tip are highly crosslinked with each other and stabilized by luminal proteins, plugs, and cap proteins at the plus ends. In the tip region, the central pair lacks typical projections and twists significantly. By analyzing cells lacking a ciliary tip-enriched protein CEP104/FAP256 by cryo-electron tomography and proteomics, we discovered candidates for the central pair cap complex and explained the potential functions of CEP104/FAP256. These data provide new insights into the function of the ciliary tip and the mechanisms of ciliary assembly and length regulation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40896.map.gz | 49.4 MB | EMDB map data format | |
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Header (meta data) | emd-40896-v30.xml emd-40896.xml | 12.1 KB 12.1 KB | Display Display | EMDB header |
Images | emd_40896.png | 103.2 KB | ||
Filedesc metadata | emd-40896.cif.gz | 3.8 KB | ||
Others | emd_40896_half_map_1.map.gz emd_40896_half_map_2.map.gz | 49.8 MB 49.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40896 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40896 | HTTPS FTP |
-Validation report
Summary document | emd_40896_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_40896_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_40896_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | emd_40896_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40896 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40896 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_40896.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 4.24 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_40896_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_40896_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Consensus map obtained by subtomogram averaging of the ciliary ti...
Entire | Name: Consensus map obtained by subtomogram averaging of the ciliary tip central pair |
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Components |
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-Supramolecule #1: Consensus map obtained by subtomogram averaging of the ciliary ti...
Supramolecule | Name: Consensus map obtained by subtomogram averaging of the ciliary tip central pair type: organelle_or_cellular_component / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Tetrahymena thermophila (eukaryote) / Strain: CU428 / 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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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 4.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 12.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 11534 |
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Extraction | Number tomograms: 144 / Number images used: 11980 |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |