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- PDB-8bbf: Structure of the IFT-A complex; IFT-A1 module -

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Basic information

Entry
Database: PDB / ID: 8bbf
TitleStructure of the IFT-A complex; IFT-A1 module
Components
  • Intraflagellar transport protein 122 homolog
  • Intraflagellar transport protein 140 homolog
  • WD repeat-containing protein 19
KeywordsTRANSPORT PROTEIN / cilia / intraflagellar transport / membrane protein import / complex
Function / homology
Function and homology information


smoothened signaling pathway involved in dorsal/ventral neural tube patterning / myotome development / ear morphogenesis / intraciliary anterograde transport / intraciliary transport particle A / cone photoreceptor outer segment / digestive system development / embryonic heart tube left/right pattern formation / embryonic body morphogenesis / photoreceptor cell outer segment organization ...smoothened signaling pathway involved in dorsal/ventral neural tube patterning / myotome development / ear morphogenesis / intraciliary anterograde transport / intraciliary transport particle A / cone photoreceptor outer segment / digestive system development / embryonic heart tube left/right pattern formation / embryonic body morphogenesis / photoreceptor cell outer segment organization / neural tube patterning / protein localization to ciliary membrane / intraciliary retrograde transport / establishment of protein localization to organelle / embryonic camera-type eye development / intraciliary transport / gonad development / spinal cord dorsal/ventral patterning / regulation of cilium assembly / photoreceptor connecting cilium / ciliary tip / Intraflagellar transport / camera-type eye morphogenesis / embryonic cranial skeleton morphogenesis / regulation of smoothened signaling pathway / embryonic brain development / non-motile cilium assembly / protein localization to cilium / non-motile cilium / nervous system process / embryonic heart tube development / embryonic forelimb morphogenesis / motile cilium / determination of left/right symmetry / embryonic limb morphogenesis / limb development / receptor clustering / embryonic digit morphogenesis / axoneme / photoreceptor outer segment / cilium assembly / Hedgehog 'off' state / negative regulation of smoothened signaling pathway / centriole / ciliary basal body / neural tube closure / cell morphogenesis / cilium / heart development / protein-containing complex assembly / in utero embryonic development / cytoskeleton / intracellular signal transduction / centrosome / membrane / plasma membrane / cytoplasm
Similarity search - Function
WDR19, WD40 repeat / WD repeat-containing protein 19/dyf-2 / WD domain, G-beta repeat / Intraflagellar transport protein 122 homolog / 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 ...WDR19, WD40 repeat / WD repeat-containing protein 19/dyf-2 / WD domain, G-beta repeat / Intraflagellar transport protein 122 homolog / 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
WD repeat-containing protein 19 / Intraflagellar transport protein 140 homolog / Intraflagellar transport protein 122 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8 Å
AuthorsHesketh, S.J. / Mukhopadhyay, A.G. / Nakamura, D. / Toropova, K. / Roberts, A.J.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Wellcome Trust202679/Z/16/Z United Kingdom
Wellcome Trust206166/Z/17/Z United Kingdom
Wellcome Trust217186/Z/19/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S007202/1 United Kingdom
CitationJournal: Cell / Year: 2022
Title: IFT-A structure reveals carriages for membrane protein transport into cilia.
Authors: Sophie J Hesketh / Aakash G Mukhopadhyay / Dai Nakamura / Katerina Toropova / Anthony J Roberts /
Abstract: Intraflagellar transport (IFT) trains are massive molecular machines that traffic proteins between cilia and the cell body. Each IFT train is a dynamic polymer of two large complexes (IFT-A and -B) ...Intraflagellar transport (IFT) trains are massive molecular machines that traffic proteins between cilia and the cell body. Each IFT train is a dynamic polymer of two large complexes (IFT-A and -B) and motor proteins, posing a formidable challenge to mechanistic understanding. Here, we reconstituted the complete human IFT-A complex and obtained its structure using cryo-EM. Combined with AlphaFold prediction and genome-editing studies, our results illuminate how IFT-A polymerizes, interacts with IFT-B, and uses an array of β-propeller and TPR domains to create "carriages" of the IFT train that engage TULP adaptor proteins. We show that IFT-A⋅TULP carriages are essential for cilia localization of diverse membrane proteins, as well as ICK-the key kinase regulating IFT train turnaround. These data establish a structural link between IFT-A's distinct functions, provide a blueprint for IFT-A in the train, and shed light on how IFT evolved from a proto-coatomer ancestor.
History
DepositionOct 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 4, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jul 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

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Assembly

Deposited unit
A: WD repeat-containing protein 19
B: Intraflagellar transport protein 140 homolog
C: Intraflagellar transport protein 122 homolog


Theoretical massNumber of molelcules
Total (without water)462,9753
Polymers462,9753
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5550 Å2
ΔGint-19 kcal/mol
Surface area110670 Å2
MethodPISA

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Components

#1: Protein WD repeat-containing protein 19 / Intraflagellar transport 144 homolog


Mass: 153639.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR19, IFT144, KIAA1638 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8NEZ3
#2: Protein Intraflagellar transport protein 140 homolog / WD and tetratricopeptide repeats protein 2


Mass: 167328.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFT140, KIAA0590, WDTC2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96RY7
#3: Protein Intraflagellar transport protein 122 homolog / WD repeat-containing protein 10 / WD repeat-containing protein 140


Mass: 142007.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFT122, SPG, WDR10, WDR140 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9HBG6

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: IFT-A complex; IFT-A1 module / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
Details: Average electron dose for additional dataset was 49.5 (e-/A2)

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Processing

EM softwareName: EPU / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136617 / Details: Resolution range 7-15A / Symmetry type: POINT

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