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- PDB-8bda: IFTA complex in anterograde intraflagellar transport trains (Chla... -

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Basic information

Entry
Database: PDB / ID: 8bda
TitleIFTA complex in anterograde intraflagellar transport trains (Chlamydomonas reinhardtii)
Components
  • Intraflagellar transport particle protein 140
  • Intraflagellar transport protein 121
  • Intraflagellar transport protein 122 homolog
  • Intraflagellar transport protein 139
  • Intraflagellar transport protein 144
KeywordsPROTEIN TRANSPORT / Cilia / IFT / Intraflagellar / transport
Function / homology
Function and homology information


intraciliary transport particle A / cellular component assembly / intraciliary retrograde transport / protein localization to cilium / non-motile cilium assembly / ciliary plasm / non-motile cilium / motile cilium / axoneme / RNA processing ...intraciliary transport particle A / cellular component assembly / intraciliary retrograde transport / protein localization to cilium / non-motile cilium assembly / ciliary plasm / non-motile cilium / motile cilium / axoneme / RNA processing / cilium / ciliary basal body
Similarity search - Function
: / IFT122, zinc ribbon domain / Tetratricopeptide repeat protein 21A/21B / : / : / : / : / : / Tetratricopeptide repeat protein 21 ARM repeat / Tetratricopeptide repeat protein 21 second ARM domain ...: / IFT122, zinc ribbon domain / Tetratricopeptide repeat protein 21A/21B / : / : / : / : / : / Tetratricopeptide repeat protein 21 ARM repeat / Tetratricopeptide repeat protein 21 second ARM domain / Tetratricopeptide repeat protein 21 N-terminal ARM repeat / Tetratricopeptide repeat protein 21 C-terminal ARM domain / TT21 fifth ARM repeats domain / Tetratricopeptide repeat protein 21 forth ARM domain / WD repeat protein 35 / WDR19, WD40 repeat / WD repeat-containing protein 19/dyf-2 / : / : / : / : / : / WDR19 second beta-propeller / IFT140 first beta-propeller / IFT140 second beta-propeller / WDR19 first beta-propeller / WDR35 second beta-propeller / IF140 C-terminal TPR domain / WDR35/TULP4 N-terminal / WD repeat-containing protein 35, TPR repeats / : / : / IFT121, second zinc finger domain / IF140/IFT172 TPR domain / : / IFT80/172/WDR35/WDR19 TPR domain / Intraflagellar transport protein 122 homolog / : / : / IFT122 second beta-propeller / IFT122 first beta-propeller / IFT122, TPR domain / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / Tetratricopeptide repeat / Quinoprotein alcohol dehydrogenase-like superfamily / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Uncharacterized protein / Intraflagellar transport protein 121 / Intraflagellar transport protein 139 / Intraflagellar transport protein 144 / Intraflagellar transport protein 122 homolog
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 20.7 Å
AuthorsLacey, S.E. / Foster, H.E. / Pigino, G.
Funding supportEuropean Union, Italy, 2items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Other government Italy
CitationJournal: 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
DepositionOct 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jul 26, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.pdb_format_compatible
Revision 1.4Jul 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Intraflagellar transport protein 121
E: Intraflagellar transport protein 139
G: Intraflagellar transport particle protein 140
I: Intraflagellar transport protein 144
L: Intraflagellar transport protein 122 homolog


Theoretical massNumber of molelcules
Total (without water)736,2775
Polymers736,2775
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area13930 Å2
ΔGint-44 kcal/mol
Surface area240430 Å2
MethodPISA

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Components

#1: Protein Intraflagellar transport protein 121


Mass: 136267.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JFR3
#2: Protein Intraflagellar transport protein 139


Mass: 152227.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A9XPA6
#3: Protein Intraflagellar transport particle protein 140


Mass: 157426.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DGM1
#4: Protein Intraflagellar transport protein 144


Mass: 150972.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A9XPA7
#5: Protein Intraflagellar transport protein 122 homolog


Mass: 139382.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: H9CTG6

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: One IFTA repeat from anterograde intraflagellar transport trains within native Chlamydomonas reinhardtii cilia
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Buffer solutionpH: 7 / Details: TAP (Tris-Acetate-Phosphate) Media
SpecimenEmbedding 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.
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 2500 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron 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

SoftwareName: UCSF ChimeraX / Version: 1.4/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package
EM software
IDNameVersionCategory
7NAMDNAMDinatormodel fitting
9PHENIXmodel refinement
13RELION3.1.33D reconstruction
14Warp3D reconstruction
CTF correctionDetails: Warp/Relion/M - CTF Refinement in M / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 20.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3897 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 600 / Num. of volumes extracted: 3897
Atomic model buildingProtocol: FLEXIBLE FIT

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