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Yorodumi- EMDB-15261: Composite map of the C. reinhardtii IFT (segment of a fully assem... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15261 | ||||||||||||||||||||||||
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Title | Composite map of the C. reinhardtii IFT (segment of a fully assembled train) at the ciliary transition zone | ||||||||||||||||||||||||
Map data | Composite map with all IFT densities | ||||||||||||||||||||||||
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 / PROTEIN TRANSPORT | ||||||||||||||||||||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||||||||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 29.9 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_15261.map.gz | 1.2 MB | EMDB map data format | |
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Header (meta data) | emd-15261-v30.xml emd-15261.xml | 20.1 KB 20.1 KB | Display Display | EMDB header |
Images | emd_15261.png | 96.9 KB | ||
Filedesc metadata | emd-15261.cif.gz | 4.9 KB | ||
Others | emd_15261_additional_1.map.gz emd_15261_additional_2.map.gz emd_15261_additional_3.map.gz | 420.8 KB 683.3 KB 475.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15261 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15261 | 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_15261.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Composite map with all IFT densities | ||||||||||||||||||||
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: Composite map: component IFT-A
File | emd_15261_additional_1.map | ||||||||||||
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Annotation | Composite map: component IFT-A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Composite map: component IFT-B
File | emd_15261_additional_2.map | ||||||||||||
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Annotation | Composite map: component IFT-B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Composite map: component dynein-1b
File | emd_15261_additional_3.map | ||||||||||||
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Annotation | Composite map: component dynein-1b | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The IFT complex (IFT-A, IFT-B and dynein-1b) at the C. reinhardti...
Entire | Name: The IFT complex (IFT-A, IFT-B and dynein-1b) at the C. reinhardtii ciliary transition zone |
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Components |
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-Supramolecule #1: The IFT complex (IFT-A, IFT-B and dynein-1b) at the C. reinhardti...
Supramolecule | Name: The IFT complex (IFT-A, IFT-B and dynein-1b) 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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 42000 |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 100.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Extraction | Number tomograms: 19 / Number images used: 553 / Software - Name: IMOD |
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Final angle assignment | Type: PROJECTION MATCHING / Software - Name: STOPGAP (ver. 0.3) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 29.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: STOPGAP (ver. 0.3) Details: Composite map generated from three separate subtomogram averages IFT-A: 571 particles, 27.3 A IFT-B: 1361 particles, 24.4 A Dynein-1b: 146 particles, 29.9 A Number subtomograms used: 146 |