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Yorodumi- EMDB-15259: In situ subtomogram average of C. reinhardtii IFT-A at the ciliar... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15259 | ||||||||||||||||||||||||
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Title | In situ subtomogram average of C. reinhardtii IFT-A at the ciliary transition zone | ||||||||||||||||||||||||
Map data | |||||||||||||||||||||||||
Sample |
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Keywords | cilia / transition zone / flagella / ciliary pore / intraflagellar transport / motility / signaling / basal body / microtubules / chlamydomonas / membrane proteins / membrane / trafficking / IFT trains / IFT / kinesin / dynein / motor protein / STRUCTURAL PROTEIN | ||||||||||||||||||||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||||||||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 27.3 Å | ||||||||||||||||||||||||
Authors | van den Hoek HG / Jordan MA / Alvarez Viar G / Righetto RD / Schaffer M / Erdmann PS / Wan WN / Plitzko JM / Baumeister W / Pigino G / Engel BD | ||||||||||||||||||||||||
Funding support | European Union, Germany, Switzerland, 7 items
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Citation | Journal: Science / Year: 2022 Title: In situ architecture of the ciliary base reveals the stepwise assembly of intraflagellar transport trains. Authors: Hugo van den Hoek / Nikolai Klena / Mareike A Jordan / Gonzalo Alvarez Viar / Ricardo D Righetto / Miroslava Schaffer / Philipp S Erdmann / William Wan / Stefan Geimer / Jürgen M Plitzko / ...Authors: Hugo van den Hoek / Nikolai Klena / Mareike A Jordan / Gonzalo Alvarez Viar / Ricardo D Righetto / Miroslava Schaffer / Philipp S Erdmann / William Wan / Stefan Geimer / Jürgen M Plitzko / Wolfgang Baumeister / Gaia Pigino / Virginie Hamel / Paul Guichard / Benjamin D Engel / Abstract: The cilium is an antenna-like organelle that performs numerous cellular functions, including motility, sensing, and signaling. The base of the cilium contains a selective barrier that regulates the ...The cilium is an antenna-like organelle that performs numerous cellular functions, including motility, sensing, and signaling. The base of the cilium contains a selective barrier that regulates the entry of large intraflagellar transport (IFT) trains, which carry cargo proteins required for ciliary assembly and maintenance. However, the native architecture of the ciliary base and the process of IFT train assembly remain unresolved. In this work, we used in situ cryo-electron tomography to reveal native structures of the transition zone region and assembling IFT trains at the ciliary base in . We combined this direct cellular visualization with ultrastructure expansion microscopy to describe the front-to-back stepwise assembly of IFT trains: IFT-B forms the backbone, onto which bind IFT-A, dynein-1b, and finally kinesin-2 before entry into the cilium. | ||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15259.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-15259-v30.xml emd-15259.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
Images | emd_15259.png | 57.8 KB | ||
Masks | emd_15259_msk_1.map | 8 MB | Mask map | |
Filedesc metadata | emd-15259.cif.gz | 4.8 KB | ||
Others | emd_15259_half_map_1.map.gz emd_15259_half_map_2.map.gz | 7.4 MB 7.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15259 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15259 | HTTPS FTP |
-Validation report
Summary document | emd_15259_validation.pdf.gz | 925.2 KB | Display | EMDB validaton report |
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Full document | emd_15259_full_validation.pdf.gz | 924.8 KB | Display | |
Data in XML | emd_15259_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | emd_15259_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15259 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15259 | 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_15259.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.84 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15259_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15259_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15259_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : IFT-A at the C. reinhardtii ciliary transition zone
Entire | Name: IFT-A at the C. reinhardtii ciliary transition zone |
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Components |
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-Supramolecule #1: IFT-A at the C. reinhardtii ciliary transition zone
Supramolecule | Name: IFT-A at the C. reinhardtii ciliary transition zone / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) / Strain: CC-3994 / Organelle: Cilium |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 100.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 42000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 27.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: STOPGAP (ver. 0.3) / Number subtomograms used: 571 |
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Extraction | Number tomograms: 19 / Number images used: 1530 |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: STOPGAP (ver. 0.3) |