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Yorodumi- PDB-8bd7: IFTB1 subcomplex of anterograde Intraflagellar transport trains (... -
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-Basic information
Entry | Database: PDB / ID: 8bd7 | |||||||||
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Title | IFTB1 subcomplex of anterograde Intraflagellar transport trains (Chlamydomonas reinhardtii) | |||||||||
Components |
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Keywords | PROTEIN TRANSPORT / Cilia / IFT / Intraflagellar / transport | |||||||||
Function / homology | Function and homology information intraciliary transport particle B binding / intraciliary transport involved in cilium assembly / intraciliary transport particle B / outer dynein arm assembly / cilium-dependent cell motility / intraciliary transport / regulation of cilium assembly / axoneme assembly / axonemal microtubule / cilium organization ...intraciliary transport particle B binding / intraciliary transport involved in cilium assembly / intraciliary transport particle B / outer dynein arm assembly / cilium-dependent cell motility / intraciliary transport / regulation of cilium assembly / axoneme assembly / axonemal microtubule / cilium organization / non-motile cilium assembly / non-motile cilium / motile cilium / ciliary membrane / ciliary base / post-transcriptional regulation of gene expression / beta-tubulin binding / axoneme / kinesin binding / cilium assembly / regulation of microtubule cytoskeleton organization / centriole / tubulin binding / ciliary basal body / regulation of protein stability / cilium / protein transport / apical part of cell / microtubule binding / cytoskeleton / protein stabilization / cytoplasm Similarity search - Function | |||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9.9 Å | |||||||||
Authors | Lacey, S.E. / Foster, H.E. / Pigino, G. | |||||||||
Funding support | European Union, Italy, 2items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bd7.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8bd7.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8bd7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bd7_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8bd7_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8bd7_validation.xml.gz | 275.6 KB | Display | |
Data in CIF | 8bd7_validation.cif.gz | 420.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/8bd7 ftp://data.pdbj.org/pub/pdb/validation_reports/bd/8bd7 | HTTPS FTP |
-Related structure data
Related structure data | 15977MC 8bdaC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 6 types, 12 molecules AHBJCKLTWYXZ
#1: Protein | Mass: 86418.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JCJ2 #2: Protein | Mass: 50453.184 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q946G4 #3: Protein | Mass: 74248.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8ITN7 #9: Protein | Mass: 49733.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CQB1 #11: Protein | Mass: 15658.664 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q8LLV9 #12: Protein | Mass: 54437.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JBY2 |
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-Intraflagellar transport protein ... , 7 types, 14 molecules DNEOFPGQIRMUSV
#4: Protein | Mass: 37976.410 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A2T2X4 #5: Protein | Mass: 63485.508 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JA42 #6: Protein | Mass: 77186.484 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q68RJ5 #7: Protein | Mass: 71648.398 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q6RCE1 #8: Protein | Mass: 85782.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A5Z0S9 #10: Protein | Mass: 51298.414 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q2XQY7 #13: Protein | Mass: 197851.172 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q5DM57 |
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-Details
Has protein modification | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: Two IFTB repeats from anterograde intraflagellar transport trains within native Chlamydomonas reinhardtii cilia Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) |
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. |
Specimen support | Grid material: GOLD / Grid type: Quantifoil R3.5/1 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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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: 9.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18216 / Symmetry type: POINT | ||||||||||||||||||||||||
EM volume selection | Num. of tomograms: 600 / Num. of volumes extracted: 18216 | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT | ||||||||||||||||||||||||
Refine LS restraints |
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