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Yorodumi- EMDB-16014: Subtomogram average of complete IFTB complex (before focussed ref... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16014 | |||||||||
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Title | Subtomogram average of complete IFTB complex (before focussed refinements of IFTB1/2) for consensus map generation | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Cilia / IFT / Intraflagellar / transport / PROTEIN TRANSPORT | |||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 14.1 Å | |||||||||
Authors | Lacey SE / Foster HE / Pigino G | |||||||||
Funding support | European Union, Italy, 2 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 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 | emd_16014.map.gz | 945.3 KB | EMDB map data format | |
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Header (meta data) | emd-16014-v30.xml emd-16014.xml | 15.5 KB 15.5 KB | Display Display | EMDB header |
Images | emd_16014.png | 43.6 KB | ||
Masks | emd_16014_msk_1.map | 10.5 MB | Mask map | |
Filedesc metadata | emd-16014.cif.gz | 4.2 KB | ||
Others | emd_16014_half_map_1.map.gz emd_16014_half_map_2.map.gz | 7.9 MB 7.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16014 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16014 | HTTPS FTP |
-Validation report
Summary document | emd_16014_validation.pdf.gz | 688.9 KB | Display | EMDB validaton report |
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Full document | emd_16014_full_validation.pdf.gz | 688.4 KB | Display | |
Data in XML | emd_16014_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | emd_16014_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16014 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16014 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16014.map.gz / Format: CCP4 / Size: 10.5 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: 6.06 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16014_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16014_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16014_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-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: Chlamydomonas reinhardtii (plant) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | helical array |
-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. |
-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: FIELD EMISSION GUN |
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 |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 14.1 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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