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- PDB-8bd7: IFTB1 subcomplex of anterograde Intraflagellar transport trains (... -

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Basic information

Entry
Database: PDB / ID: 8bd7
TitleIFTB1 subcomplex of anterograde Intraflagellar transport trains (Chlamydomonas reinhardtii)
Components
  • (Intraflagellar transport protein ...) x 7
  • Clusterin-associated protein 1
  • IFT54
  • IFT70
  • IFT88
  • Intraflagellar transport particle protein IFT20
  • Osm-6-like protein
KeywordsPROTEIN 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 ...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 / kinesin binding / axoneme / 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
Clusterin-associated protein-1 / Intra-flagellar transport protein 57 / Intraflagellar transport protein 20 / Tetratricopeptide repeat protein 26 / 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 / Tetratricopeptide repeat protein 26 / 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 / Intraflagellar transport protein 52, C-terminal domain / ABC-type uncharacterised transport system / Intraflagellar transport protein 81 / IFT81, calponin homology domain / IFT81, N-terminal domain superfamily / ABC-type uncharacterized transport system / 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 / TRAF3-interacting protein 1 / Tetratricopeptide repeat / Quinoprotein amine dehydrogenase, beta chain-like / Tetratricopeptide repeat / Tetratricopeptide repeat / IQ motif, EF-hand binding site / Class I glutamine amidotransferase-like / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Clusterin-associated protein 1 / Intraflagellar transport protein 46 / Intraflagellar transport protein 80 / Uncharacterized protein / Intraflagellar transport protein 56 / Uncharacterized protein / Intraflagellar transport protein 88 / Intraflagellar transport protein 57 / Intraflagellar transport protein 172 / Intraflagellar transport protein 81 ...Clusterin-associated protein 1 / Intraflagellar transport protein 46 / Intraflagellar transport protein 80 / Uncharacterized protein / Intraflagellar transport protein 56 / Uncharacterized protein / Intraflagellar transport protein 88 / 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: 9.9 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 17, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2May 24, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3May 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 1.4Jul 26, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.pdb_format_compatible

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IFT88
B: Osm-6-like protein
C: IFT70
D: Intraflagellar transport protein 46
E: Intraflagellar transport protein 56
F: Intraflagellar transport protein 81
G: Intraflagellar transport protein 74
I: Intraflagellar transport protein 80
L: Clusterin-associated protein 1
M: Intraflagellar transport protein 57
W: Intraflagellar transport particle protein IFT20
X: IFT54
S: Intraflagellar transport protein 172
H: IFT88
J: Osm-6-like protein
K: IFT70
N: Intraflagellar transport protein 46
O: Intraflagellar transport protein 56
P: Intraflagellar transport protein 81
Q: Intraflagellar transport protein 74
R: Intraflagellar transport protein 80
T: Clusterin-associated protein 1
U: Intraflagellar transport protein 57
Y: Intraflagellar transport particle protein IFT20
Z: IFT54
V: Intraflagellar transport protein 172


Theoretical massNumber of molelcules
Total (without water)1,832,35826
Polymers1,832,35826
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area123670 Å2
ΔGint-621 kcal/mol
Surface area535200 Å2
MethodPISA

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Components

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Protein , 6 types, 12 molecules AHBJCKLTWYXZ

#1: 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
#2: 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
#3: 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
#9: 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
#11: 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
#12: 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

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Intraflagellar transport protein ... , 7 types, 14 molecules DNEOFPGQIRMUSV

#4: 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
#5: Protein Intraflagellar transport protein 56 / Abnormal dye filling protein 13 / Tetratricopeptide repeat protein 26 homolog / TPR repeat protein 26 homolog


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 Intraflagellar transport protein 81


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 Intraflagellar transport protein 74 / Intraflagellar transport protein 71 / IFT-71 / Intraflagellar transport protein 72 / IFT74/72


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 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
#10: Protein Intraflagellar transport protein 57


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 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

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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: Two IFTB repeats 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.
Specimen supportGrid material: GOLD / Grid type: Quantifoil R3.5/1
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: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategory
7NAMDNAMDinatormodel fitting
12RELION3.1.33D reconstruction
13Warp3D reconstruction
14PHENIXmodel refinement
CTF correctionDetails: Warp/Relion/M - CTF Refinement in M / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 9.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18216 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 600 / Num. of volumes extracted: 18216
Atomic model buildingProtocol: FLEXIBLE FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00487924
ELECTRON MICROSCOPYf_angle_d0.882118708
ELECTRON MICROSCOPYf_dihedral_angle_d6.27511840
ELECTRON MICROSCOPYf_chiral_restr0.0512962
ELECTRON MICROSCOPYf_plane_restr0.00615460

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