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- EMDB-15979: Masked refinement of the IFTB2 subcomplex within anterograde intr... -
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Open data
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Basic information
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Title | Masked refinement of the IFTB2 subcomplex within anterograde intraflagellar trains in Chlamydomonas reinhardtii cilia | |||||||||
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![]() | Cilia / IFT / Intraflagellar / transport / PROTEIN TRANSPORT | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 11.5 Å | |||||||||
![]() | Lacey SE / Pigino G | |||||||||
Funding support | European Union, ![]()
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![]() | ![]() Title: The molecular structure of IFT-A and IFT-B in anterograde intraflagellar transport trains. Authors: Samuel E Lacey / Helen E Foster / Gaia Pigino / ![]() Abstract: Anterograde intraflagellar transport (IFT) trains are essential for cilia assembly and maintenance. These trains are formed of 22 IFT-A and IFT-B proteins that link structural and signaling cargos to ...Anterograde intraflagellar transport (IFT) trains are essential for cilia assembly and maintenance. These trains are formed of 22 IFT-A and IFT-B proteins that link structural and signaling cargos to microtubule motors for import into cilia. It remains unknown how the IFT-A/-B proteins are arranged into complexes and how these complexes polymerize into functional trains. Here we use in situ cryo-electron tomography of Chlamydomonas reinhardtii cilia and AlphaFold2 protein structure predictions to generate a molecular model of the entire anterograde train. We show how the conformations of both IFT-A and IFT-B are dependent on lateral interactions with neighboring repeats, suggesting that polymerization is required to cooperatively stabilize the complexes. Following three-dimensional classification, we reveal how IFT-B extends two flexible tethers to maintain a connection with IFT-A that can withstand the mechanical stresses present in actively beating cilia. Overall, our findings provide a framework for understanding the fundamental processes that govern cilia assembly. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.9 KB 16.9 KB | Display Display | ![]() |
Images | ![]() | 42.9 KB | ||
Filedesc metadata | ![]() | 4.3 KB | ||
Others | ![]() ![]() ![]() | 1.2 MB 27.1 MB 27.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 701.3 KB | Display | ![]() |
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Full document | ![]() | 700.9 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 13 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.04 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Masked classification of the periphery of IFTB2 complex,...
File | emd_15979_additional_1.map | ||||||||||||
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Annotation | Masked classification of the periphery of IFTB2 complex, in the region corrresponding to IFT172 (WD domains) and IFT57 CH domain. Lowpass filtered to 18 angstrom and a b factor of -1300 A^2 applied. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15979_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15979_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Two IFTB repeats from anterograde intraflagellar transport trains...
Entire | Name: Two IFTB repeats from anterograde intraflagellar transport trains within native Chlamydomonas reinhardtii cilia |
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Components |
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-Supramolecule #1: Two IFTB repeats from anterograde intraflagellar transport trains...
Supramolecule | Name: Two IFTB repeats from anterograde intraflagellar transport trains within native Chlamydomonas reinhardtii cilia type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13 |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | helical array |
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Sample preparation
Buffer | pH: 7 / Details: TAP (Tris-Acetate-Phosphate) Media |
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Vitrification | Cryogen name: ETHANE |
Details | Chlamydomonas reinhardtii cells applied to quantifoil grids and plunge frozen; cilia project out from cell bodies and traverse holes in the carbon film. |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 2.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 11.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION (ver. 3.1.3), Warp) / Number subtomograms used: 18216 |
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Extraction | Number tomograms: 600 / Number images used: 18216 |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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