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- PDB-8fgw: Human IFT-A complex structures provide molecular insights into ci... -

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Basic information

Entry
Database: PDB / ID: 8fgw
TitleHuman IFT-A complex structures provide molecular insights into ciliary transport
Components
  • (Intraflagellar transport protein ...) x 3
  • (WD repeat-containing protein ...) x 2
  • Tetratricopeptide repeat protein 21B
KeywordsTRANSPORT PROTEIN / IFT-A complex / TULP3 / cilia
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: 3.7 Å
AuthorsJiang, M. / Palicharla, V.R. / Miller, D. / Hwang, S.H. / Zhu, H. / Hixson, P. / Mukhopadhyay, S. / Sun, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R00HL143037 United States
CitationJournal: Cell Res / Year: 2023
Title: Human IFT-A complex structures provide molecular insights into ciliary transport.
Authors: Meiqin Jiang / Vivek Reddy Palicharla / Darcie Miller / Sun-Hee Hwang / Hanwen Zhu / Patricia Hixson / Saikat Mukhopadhyay / Ji Sun /
Abstract: Intraflagellar transport (IFT) complexes, IFT-A and IFT-B, form bidirectional trains that move along the axonemal microtubules and are essential for assembling and maintaining cilia. Mutations in IFT ...Intraflagellar transport (IFT) complexes, IFT-A and IFT-B, form bidirectional trains that move along the axonemal microtubules and are essential for assembling and maintaining cilia. Mutations in IFT subunits lead to numerous ciliopathies involving multiple tissues. However, how IFT complexes assemble and mediate cargo transport lacks mechanistic understanding due to missing high-resolution structural information of the holo-complexes. Here we report cryo-EM structures of human IFT-A complexes in the presence and absence of TULP3 at overall resolutions of 3.0-3.9 Å. IFT-A adopts a "lariat" shape with interconnected core and peripheral subunits linked by structurally vital zinc-binding domains. TULP3, the cargo adapter, interacts with IFT-A through its N-terminal region, and interface mutations disrupt cargo transport. We also determine the molecular impacts of disease mutations on complex formation and ciliary transport. Our work reveals IFT-A architecture, sheds light on ciliary transport and IFT train formation, and enables the rationalization of disease mutations in ciliopathies.
History
DepositionDec 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WD repeat-containing protein 35
B: Intraflagellar transport protein 122 homolog
C: WD repeat-containing protein 19
D: Tetratricopeptide repeat protein 21B
E: Intraflagellar transport protein 140 homolog
F: Intraflagellar transport protein 43 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)767,88711
Polymers767,5606
Non-polymers3275
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 AC

#1: Protein WD repeat-containing protein 35 / Intraflagellar transport protein 121 homolog


Mass: 133705.641 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: Homo sapiens (human) / References: UniProt: Q9P2L0
#3: Protein WD repeat-containing protein 19 / Intraflagellar transport 144 homolog


Mass: 151760.391 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: Homo sapiens (human) / References: UniProt: Q8NEZ3

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

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


Mass: 141993.703 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: Homo sapiens (human) / References: UniProt: Q9HBG6
#5: Protein Intraflagellar transport protein 140 homolog / / WD and tetratricopeptide repeats protein 2


Mass: 165404.281 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: Homo sapiens (human) / References: UniProt: Q96RY7
#6: Protein Intraflagellar transport protein 43 homolog /


Mass: 23558.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFT43, C14orf179 / Production host: Homo sapiens (human) / References: UniProt: Q96FT9

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Protein / Non-polymers , 2 types, 6 molecules D

#4: Protein Tetratricopeptide repeat protein 21B / / TPR repeat protein 21B / Intraflagellar transport 139 homolog


Mass: 151137.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTC21B, IFT139, KIAA1992, Nbla10696 / Production host: Homo sapiens (human) / References: UniProt: Q7Z4L5
#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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: Intraflagellar transport complex A (IFT-A) / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
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: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 66 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67560 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00344410
ELECTRON MICROSCOPYf_angle_d0.51860133
ELECTRON MICROSCOPYf_dihedral_angle_d4.5556012
ELECTRON MICROSCOPYf_chiral_restr0.0416736
ELECTRON MICROSCOPYf_plane_restr0.0037711

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