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- PDB-8bbe: Structure of the IFT-A complex; IFT-A2 module -

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Basic information

Entry
Database: PDB / ID: 8bbe
TitleStructure of the IFT-A complex; IFT-A2 module
Components
  • Intraflagellar transport protein 122 homolog
  • Intraflagellar transport protein 43 homolog
  • SNAP-tag,Tetratricopeptide repeat protein 21B
  • WD repeat-containing protein 35
KeywordsTRANSPORT PROTEIN / cilia / intraflagellar transport / membrane protein import / complex
Function / homology
Function and homology information


protein localization to non-motile cilium / regulation of intraciliary retrograde transport / : / forebrain dorsal/ventral pattern formation / intraciliary transport particle A / intraciliary anterograde transport / negative regulation of eating behavior / embryonic heart tube left/right pattern formation / embryonic body morphogenesis / intraciliary retrograde transport ...protein localization to non-motile cilium / regulation of intraciliary retrograde transport / : / forebrain dorsal/ventral pattern formation / intraciliary transport particle A / intraciliary anterograde transport / negative regulation of eating behavior / embryonic heart tube left/right pattern formation / embryonic body morphogenesis / intraciliary retrograde transport / cerebellar Purkinje cell differentiation / intraciliary transport / establishment of protein localization to organelle / spinal cord dorsal/ventral patterning / photoreceptor connecting cilium / ciliary tip / ventricular system development / Intraflagellar transport / camera-type eye morphogenesis / protein localization to cilium / non-motile cilium assembly / non-motile cilium / embryonic heart tube development / regulation of smoothened signaling pathway / embryonic forelimb morphogenesis / limb development / smoothened signaling pathway / axoneme / Bergmann glial cell differentiation / cilium assembly / centriolar satellite / Hedgehog 'off' state / negative regulation of smoothened signaling pathway / centriole / cellular response to leukemia inhibitory factor / ciliary basal body / neural tube closure / cilium / positive regulation of canonical Wnt signaling pathway / microtubule cytoskeleton / cytoskeleton / centrosome / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / membrane / cytoplasm
Similarity search - Function
Intraflagellar transport protein 43 / Intraflagellar transport protein 43 / Tetratricopeptide repeat protein 21A/21B / WD repeat protein 35 / Intraflagellar transport protein 122 homolog / Tetratricopeptide repeat / Tetratricopeptide repeat / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Tetratricopeptide repeat ...Intraflagellar transport protein 43 / Intraflagellar transport protein 43 / Tetratricopeptide repeat protein 21A/21B / WD repeat protein 35 / Intraflagellar transport protein 122 homolog / Tetratricopeptide repeat / Tetratricopeptide repeat / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Tetratricopeptide repeat protein 21B / Intraflagellar transport protein 43 homolog / Intraflagellar transport protein 122 homolog / WD repeat-containing protein 35
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Intraflagellar transport protein 122 homolog
D: SNAP-tag,Tetratricopeptide repeat protein 21B
E: WD repeat-containing protein 35
F: Intraflagellar transport protein 43 homolog


Theoretical massNumber of molelcules
Total (without water)470,0194
Polymers470,0194
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Intraflagellar transport protein 122 homolog / / WD repeat-containing protein 10 / WD repeat-containing protein 140


Mass: 141713.500 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
#2: Protein SNAP-tag,Tetratricopeptide repeat protein 21B / TPR repeat protein 21B / Intraflagellar transport 139 homolog


Mass: 170652.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MGMT, TTC21B, IFT139, KIAA1992, Nbla10696 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q7Z4L5
#3: Protein WD repeat-containing protein 35 / Intraflagellar transport protein 121 homolog


Mass: 134037.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR35, IFT121, KIAA1336 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9P2L0
#4: Protein Intraflagellar transport protein 43 homolog /


Mass: 23615.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFT43, C14orf179 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96FT9

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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-A2 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 FIELDBright-field microscopy / 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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 242645 / Details: Resolution range 3.2-8A / Symmetry type: POINT

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