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- PDB-8bbg: Structure of the IFT-A complex; anterograde IFT-A train model -

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Basic information

Entry
Database: PDB / ID: 8bbg
TitleStructure of the IFT-A complex; anterograde IFT-A train model
Components
  • (Intraflagellar transport protein ...) x 3
  • (WD repeat-containing protein ...) x 2
  • SNAP-tag,Tetratricopeptide repeat protein 21B
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 / protein localization to non-motile cilium / regulation of intraciliary retrograde transport / : / forebrain dorsal/ventral pattern formation / ear morphogenesis / intraciliary transport particle A / intraciliary anterograde transport / cone photoreceptor outer segment ...smoothened signaling pathway involved in dorsal/ventral neural tube patterning / myotome development / protein localization to non-motile cilium / regulation of intraciliary retrograde transport / : / forebrain dorsal/ventral pattern formation / ear morphogenesis / intraciliary transport particle A / intraciliary anterograde transport / cone photoreceptor outer segment / negative regulation of eating behavior / digestive system development / embryonic heart tube left/right pattern formation / embryonic body morphogenesis / photoreceptor cell outer segment organization / neural tube patterning / intraciliary retrograde transport / protein localization to ciliary membrane / cerebellar Purkinje cell differentiation / embryonic camera-type eye development / intraciliary transport / establishment of protein localization to organelle / gonad development / regulation of cilium assembly / spinal cord dorsal/ventral patterning / photoreceptor connecting cilium / ciliary tip / ventricular system development / Intraflagellar transport / camera-type eye morphogenesis / embryonic brain development / protein localization to cilium / non-motile cilium assembly / non-motile cilium / embryonic heart tube development / regulation of smoothened signaling pathway / embryonic cranial skeleton morphogenesis / nervous system process / motile cilium / embryonic forelimb morphogenesis / determination of left/right symmetry / embryonic limb morphogenesis / limb development / smoothened signaling pathway / embryonic digit morphogenesis / receptor clustering / axoneme / Bergmann glial cell differentiation / cilium assembly / centriolar satellite / photoreceptor outer segment / Hedgehog 'off' state / negative regulation of smoothened signaling pathway / centriole / cellular response to leukemia inhibitory factor / ciliary basal body / neural tube closure / cell morphogenesis / cilium / positive regulation of canonical Wnt signaling pathway / microtubule cytoskeleton / heart development / protein-containing complex assembly / in utero embryonic development / cytoskeleton / centrosome / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / membrane / plasma membrane / cytoplasm
Similarity search - Function
Intraflagellar transport protein 43 / Intraflagellar transport protein 43 / Tetratricopeptide repeat protein 21A/21B / WD repeat protein 35 / WDR19, WD40 repeat / WD repeat-containing protein 19/dyf-2 / WD domain, G-beta repeat / Intraflagellar transport protein 122 homolog / Tetratricopeptide repeat / Tetratricopeptide repeat ...Intraflagellar transport protein 43 / Intraflagellar transport protein 43 / Tetratricopeptide repeat protein 21A/21B / WD repeat protein 35 / WDR19, WD40 repeat / WD repeat-containing protein 19/dyf-2 / WD domain, G-beta repeat / 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 / WD repeat-containing protein 19 / Intraflagellar transport protein 43 homolog / Intraflagellar transport protein 140 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

Downloads & links

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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
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)791,2816
Polymers791,2816
Non-polymers00
Water0
1


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

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Components

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WD repeat-containing protein ... , 2 types, 2 molecules AE

#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
#5: 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

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Intraflagellar transport protein ... , 3 types, 3 molecules BCF

#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
#6: 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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Protein , 1 types, 1 molecules D

#4: 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, methylated-DNA-[protein]-cysteine S-methyltransferase

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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 / 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
VitrificationCryogen 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 242645
Details: Above value for the IFT-A2 module map (EMD-15954), resolution range 3.2-8A. For the IFT-A1 module map (EMD-15955), number of particles used was 136617 with map resolution range 7-15 A.
Symmetry type: POINT
Atomic model buildingDetails: To generate a 14 subunit IFT-A train polymer from PDB-8BBG please enter the following in the command line of ChimeraX: sym #1 biomt copies true newModel true

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