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- PDB-8ruy: Structure of IFTA and IFTB in Retrograde Intraflagellar transport... -

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Basic information

Entry
Database: PDB / ID: 8ruy
TitleStructure of IFTA and IFTB in Retrograde Intraflagellar transport trains
Components
  • (Intraflagellar transport particle protein ...) x 2
  • (Intraflagellar transport protein ...) x 13
  • Clusterin-associated protein 1
  • IFT54
  • IFT70
  • IFT88
  • Osm-6-like protein
KeywordsPROTEIN TRANSPORT / Cilia / IFT / train / retrograde
Function / homology
Function and homology information


intraciliary transport particle B binding / intraciliary transport particle / intraciliary transport involved in cilium assembly / intraciliary transport particle B / intraciliary transport particle A / cellular component assembly / outer dynein arm assembly / cilium-dependent cell motility / intraciliary retrograde transport / intraciliary transport ...intraciliary transport particle B binding / intraciliary transport particle / intraciliary transport involved in cilium assembly / intraciliary transport particle B / intraciliary transport particle A / cellular component assembly / outer dynein arm assembly / cilium-dependent cell motility / intraciliary retrograde transport / intraciliary transport / regulation of cilium assembly / axoneme assembly / axonemal microtubule / cilium organization / protein localization to cilium / non-motile cilium assembly / ciliary plasm / non-motile cilium / motile cilium / ciliary membrane / post-transcriptional regulation of gene expression / ciliary base / microtubule organizing center / kinesin binding / axoneme / cilium assembly / beta-tubulin binding / RNA processing / centriole / tubulin binding / regulation of microtubule cytoskeleton organization / regulation of protein stability / apical part of cell / protein transport / microtubule binding / cytoskeleton / protein stabilization / cilium / ciliary basal body / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Clusterin-associated protein-1 / Intra-flagellar transport protein 57 / Intraflagellar transport protein 20 / Clusterin-associated protein-1 / Intra-flagellar transport protein 57 / Intraflagellar transport complex B, subunit 20 / Intraflagellar transport complex B protein 46 / Intraflagellar transport protein 74 / Tetratricopeptide repeat protein 30 / : ...Clusterin-associated protein-1 / Intra-flagellar transport protein 57 / Intraflagellar transport protein 20 / Clusterin-associated protein-1 / Intra-flagellar transport protein 57 / Intraflagellar transport complex B, subunit 20 / Intraflagellar transport complex B protein 46 / Intraflagellar transport protein 74 / Tetratricopeptide repeat protein 30 / : / : / : / Intraflagellar transport complex B protein 46 C terminal / IFT80 second beta-propeller / IFT52 central domain / IFT52 GIFT domain / Intraflagellar transport protein 25 / Intraflagellar transport protein 81 / IFT81, calponin homology domain / IFT81, N-terminal domain superfamily / Intraflagellar transport 81 calponin homology domain / Intraflagellar transport protein 52 homolog / TRAF3-interacting protein 1, N-terminal / TRAF3-interacting protein 1, C-terminal domain / TRAF3-interacting protein 1, N-terminal domain superfamily / : / Microtubule-binding protein MIP-T3 CH-like domain / Microtubule-binding protein MIP-T3 C-terminal region / Intraflagellar transport protein 52, C-terminal domain / TRAF3-interacting protein 1 / : / 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 / Tetratricopeptide repeat / 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 / Ras of Complex, Roc, domain of DAPkinase / Quinoprotein amine dehydrogenase, beta chain-like / Tetratricopeptide repeat / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / Small GTPase Rab domain profile. / Quinoprotein alcohol dehydrogenase-like superfamily / Tetratricopeptide repeat / Class I glutamine amidotransferase-like / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Galactose-binding-like domain superfamily / Rab subfamily of small GTPases / Small GTP-binding protein domain / Tetratricopeptide-like helical domain superfamily / WD domain, G-beta repeat / 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 / Uncharacterized protein / Intraflagellar transport protein 46 / Intraflagellar transport protein 80 / Intraflagellar transport protein 22 / Intraflagellar transport protein 27 / Uncharacterized protein / TRAF3-interacting protein 1 / Uncharacterized protein / Intraflagellar transport protein 121 ...Uncharacterized protein / Uncharacterized protein / Intraflagellar transport protein 46 / Intraflagellar transport protein 80 / Intraflagellar transport protein 22 / Intraflagellar transport protein 27 / Uncharacterized protein / TRAF3-interacting protein 1 / Uncharacterized protein / Intraflagellar transport protein 121 / Intraflagellar transport protein 139 / Intraflagellar transport protein 144 / Intraflagellar transport protein 25 / Intraflagellar transport protein 122 homolog / Intraflagellar transport protein 57 / Intraflagellar transport protein 172 / Intraflagellar transport protein 81 / Intraflagellar transport protein 74 / Intraflagellar transport particle protein IFT20 / Osm-6-like protein
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 15.4 Å
AuthorsLacey, S. / Pigino, G.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Other government
CitationJournal: Cell / Year: 2024
Title: Extensive structural rearrangement of intraflagellar transport trains underpins bidirectional cargo transport.
Authors: Samuel E Lacey / Andrea Graziadei / Gaia Pigino /
Abstract: Bidirectional transport in cilia is carried out by polymers of the IFTA and IFTB protein complexes, called anterograde and retrograde intraflagellar transport (IFT) trains. Anterograde trains deliver ...Bidirectional transport in cilia is carried out by polymers of the IFTA and IFTB protein complexes, called anterograde and retrograde intraflagellar transport (IFT) trains. Anterograde trains deliver cargoes from the cell to the cilium tip, then convert into retrograde trains for cargo export. We set out to understand how the IFT complexes can perform these two directly opposing roles before and after conversion. We use cryoelectron tomography and in situ cross-linking mass spectrometry to determine the structure of retrograde IFT trains and compare it with the known structure of anterograde trains. The retrograde train is a 2-fold symmetric polymer organized around a central thread of IFTA complexes. We conclude that anterograde-to-retrograde remodeling involves global rearrangements of the IFTA/B complexes and requires complete disassembly of the anterograde train. Finally, we describe how conformational changes to cargo-binding sites facilitate unidirectional cargo transport in a bidirectional system.
History
DepositionJan 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update
Revision 1.2Aug 6, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Intraflagellar transport protein 144
B: Intraflagellar transport particle protein 140
H: Osm-6-like protein
J: Intraflagellar transport protein 80
K: IFT54
L: Intraflagellar transport particle protein IFT20
N: Clusterin-associated protein 1
O: Intraflagellar transport protein 74
P: Intraflagellar transport protein 81
Q: Intraflagellar transport protein 27
R: Intraflagellar transport protein 25
S: Intraflagellar transport protein 46
T: Intraflagellar transport protein 22
h: Osm-6-like protein
i: Intraflagellar transport protein 172
j: Intraflagellar transport protein 80
k: IFT54
l: Intraflagellar transport particle protein IFT20
n: Clusterin-associated protein 1
s: Intraflagellar transport protein 46
C: Intraflagellar transport protein 122 homolog
D: Intraflagellar transport protein 121
E: Intraflagellar transport protein 139
F: IFT88
G: IFT70
I: Intraflagellar transport protein 172
M: Intraflagellar transport protein 57
f: IFT88
g: IFT70
m: Intraflagellar transport protein 57


Theoretical massNumber of molelcules
Total (without water)2,357,50930
Polymers2,357,50930
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Intraflagellar transport protein ... , 13 types, 17 molecules AJjOPQRSsTiICDEMm

#1: 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
#4: Protein Intraflagellar transport protein 80


Mass: 85782.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A5Z0S9
#8: Protein Intraflagellar transport protein 74 / Intraflagellar transport protein 71 / IFT-71 / Intraflagellar transport protein 72 / IFT74/72


Mass: 71648.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q6RCE1
#9: Protein Intraflagellar transport protein 81


Mass: 77186.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q68RJ5
#10: Protein Intraflagellar transport protein 27 / Flagellar-associated protein 156


Mass: 22783.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HN58
#11: Protein Intraflagellar transport protein 25 / Flagellar-associated protein 232


Mass: 20380.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: B8LIX8
#12: Protein Intraflagellar transport protein 46 / Flagellar-associated protein 32 / IFT complex B protein


Mass: 37976.410 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A2T2X4
#13: Protein Intraflagellar transport protein 22 / Flagellar-associated protein 9


Mass: 21363.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HME3
#14: Protein Intraflagellar transport protein 172


Mass: 197851.172 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q5DM57
#15: 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
#16: 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
#17: 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
#20: Protein Intraflagellar transport protein 57


Mass: 51374.508 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q2XQY7

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Intraflagellar transport particle protein ... , 2 types, 3 molecules BLl

#2: 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
#6: Protein Intraflagellar transport particle protein IFT20


Mass: 15658.664 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q8LLV9

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Protein , 5 types, 10 molecules HhKkNnFfGg

#3: Protein Osm-6-like protein


Mass: 50453.184 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q946G4
#5: Protein IFT54


Mass: 54437.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JBY2
#7: Protein Clusterin-associated protein 1


Mass: 49733.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CQB1
#18: Protein IFT88


Mass: 86418.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JCJ2
#19: Protein IFT70


Mass: 74248.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8ITN7

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: In situ retrograde intraflagellar transport trains in dhc1b-3 mutant Chlamydomonas reinhardtii cilia
Type: CELL
Details: Temperature sensitive cells incubated at restrictive temperature (34 degrees C) for 10 hours and plunge frozen on grids.
Entity ID: #1-#2, #15-#19, #3, #14, #4-#6, #20, #7-#13 / Source: NATURAL
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: dhc1b-3
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 4000 nm / Nominal defocus min: 2000 nm
Image recordingElectron dose: 2.6 e/Å2 / Avg electron dose per subtomogram: 104 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
4CTFFIND4CTF correction
13RELION3.1.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 15.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5896
Details: Composite map, with constituent maps ranging from 15.4 to 28.3 angstrom
Symmetry type: POINT
EM volume selectionNum. of tomograms: 756 / Num. of volumes extracted: 10455

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