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- PDB-8bda: IFTA complex in anterograde intraflagellar transport trains (Chla... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bda | |||||||||
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Title | IFTA complex in anterograde intraflagellar transport trains (Chlamydomonas reinhardtii) | |||||||||
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![]() | PROTEIN TRANSPORT / Cilia / IFT / Intraflagellar / transport | |||||||||
Function / homology | ![]() intraciliary transport particle A / intraciliary retrograde transport / intraciliary transport / non-motile cilium assembly / protein localization to cilium / ciliary plasm / non-motile cilium / motile cilium / axoneme / cilium assembly ...intraciliary transport particle A / intraciliary retrograde transport / intraciliary transport / non-motile cilium assembly / protein localization to cilium / ciliary plasm / non-motile cilium / motile cilium / axoneme / cilium assembly / RNA processing / ciliary basal body / chloroplast / cilium Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 20.7 Å | |||||||||
![]() | Lacey, S.E. / Foster, H.E. / 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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 168 KB | Display | |
Data in CIF | ![]() | 257.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 15980MC ![]() 8bd7C C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 136267.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 152227.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein | Mass: 157426.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: Protein | Mass: 150972.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#5: Protein | Mass: 139382.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: subtomogram averaging |
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Sample preparation
Component | Name: One IFTA repeat from anterograde intraflagellar transport trains within native Chlamydomonas reinhardtii cilia Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7 / Details: TAP (Tris-Acetate-Phosphate) Media |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Chlamydomonas reinhardtii cells applied to quantifoil grids and plunge frozen; cilia project out from cell bodies and traverse holes in the carbon film. |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 2500 nm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 2.6 e/Å2 / Avg electron dose per subtomogram: 104 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
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Processing
Software | Name: UCSF ChimeraX / Version: 1.4/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package | ||||||||||||||||||||
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EM software |
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CTF correction | Details: Warp/Relion/M - CTF Refinement in M / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||
3D reconstruction | Resolution: 20.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3897 / Symmetry type: POINT | ||||||||||||||||||||
EM volume selection | Num. of tomograms: 600 / Num. of volumes extracted: 3897 | ||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT |