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Yorodumi- EMDB-15257: Composite map of the C. reinhardtii ciliary transition zone (full... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15257 | ||||||||||||||||||||||||
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Title | Composite map of the C. reinhardtii ciliary transition zone (full 9-fold assembly) from in situ subtomogram averaging | ||||||||||||||||||||||||
Map data | Full 9-fold symmetrical composite model of TZ structures including schematic representations of connecting MTDs, MTTs and central pair singlet MTs | ||||||||||||||||||||||||
Sample |
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Keywords | cilia / transition zone / flagella / ciliary pore / intraflagellar transport / motility / signaling / basal body / microtubules / chlamydomonas / cytoskeleton / MTD / doublet / stellate / Y-link / sleeve / STRUCTURAL PROTEIN | ||||||||||||||||||||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||||||||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 34.7 Å | ||||||||||||||||||||||||
Authors | van den Hoek HG / Righetto RD / Schaffer M / Erdmann PS / Wan WN / Plitzko JM / Baumeister W / 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_15257.map.gz | 910.3 MB | EMDB map data format | |
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Header (meta data) | emd-15257-v30.xml emd-15257.xml | 22.4 KB 22.4 KB | Display Display | EMDB header |
Images | emd_15257.png | 123.3 KB | ||
Filedesc metadata | emd-15257.cif.gz | 5 KB | ||
Others | emd_15257_additional_1.map.gz emd_15257_additional_2.map.gz emd_15257_additional_3.map.gz emd_15257_additional_4.map.gz | 496.5 MB 501.3 MB 503.3 MB 504.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15257 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15257 | HTTPS FTP |
-Validation report
Summary document | emd_15257_validation.pdf.gz | 322.9 KB | Display | EMDB validaton report |
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Full document | emd_15257_full_validation.pdf.gz | 322.5 KB | Display | |
Data in XML | emd_15257_validation.xml.gz | 4.6 KB | Display | |
Data in CIF | emd_15257_validation.cif.gz | 5.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15257 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15257 | 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_15257.map.gz / Format: CCP4 / Size: 1021.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Full 9-fold symmetrical composite model of TZ structures including schematic representations of connecting MTDs, MTTs and central pair singlet MTs | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||
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
-Additional map: 9-fold composite model: MTD Sleeve component
File | emd_15257_additional_1.map | ||||||||||||
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Annotation | 9-fold composite model: MTD Sleeve component | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 9-fold composite model: Stellate component (filaments only)
File | emd_15257_additional_2.map | ||||||||||||
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Annotation | 9-fold composite model: Stellate component (filaments only) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 9-fold composite model: Stellate component (MTDs only)
File | emd_15257_additional_3.map | ||||||||||||
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Annotation | 9-fold composite model: Stellate component (MTDs only) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 9-fold composite model: Y-link component
File | emd_15257_additional_4.map | ||||||||||||
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Annotation | 9-fold composite model: Y-link component | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Composite map of the C. reinhardtii ciliary transition zone (full...
Entire | Name: Composite map of the C. reinhardtii ciliary transition zone (full 9-fold assembly) |
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Components |
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-Supramolecule #1: Composite map of the C. reinhardtii ciliary transition zone (full...
Supramolecule | Name: Composite map of the C. reinhardtii ciliary transition zone (full 9-fold assembly) 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: C9 (9 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 34.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: STOPGAP (ver. 0.3) Details: Composite map generated from three separate subtomogram averages MTD Sleeve: 110 particles, 34.7 A Stellate: 206 particles, 28.2 A Y-link: 529 particles, 27.9 A Number subtomograms used: 110 |
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Extraction | Number tomograms: 19 / Number images used: 325 / Software - Name: IMOD |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: STOPGAP (ver. 0.3) |