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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 / regulation of intraciliary retrograde transport / forebrain dorsal/ventral pattern formation / ear morphogenesis / digestive system development / protein localization to non-motile cilium / cone photoreceptor outer segment / intraciliary anterograde transport / embryonic heart tube left/right pattern formation ...smoothened signaling pathway involved in dorsal/ventral neural tube patterning / myotome development / regulation of intraciliary retrograde transport / forebrain dorsal/ventral pattern formation / ear morphogenesis / digestive system development / protein localization to non-motile cilium / cone photoreceptor outer segment / intraciliary anterograde transport / embryonic heart tube left/right pattern formation / intraciliary transport particle A / negative regulation of eating behavior / neural tube patterning / photoreceptor cell outer segment organization / embryonic body morphogenesis / protein localization to ciliary membrane / establishment of protein localization to organelle / cerebellar Purkinje cell differentiation / embryonic camera-type eye development / intraciliary retrograde transport / spinal cord dorsal/ventral patterning / gonad development / intraciliary transport / regulation of cilium assembly / photoreceptor connecting cilium / ventricular system development / camera-type eye morphogenesis / Intraflagellar transport / embryonic cranial skeleton morphogenesis / embryonic brain development / protein localization to cilium / regulation of smoothened signaling pathway / non-motile cilium assembly / embryonic heart tube development / embryonic forelimb morphogenesis / non-motile cilium / determination of left/right symmetry / embryonic limb morphogenesis / motile cilium / nervous system process / perinuclear theca / embryonic digit morphogenesis / smoothened signaling pathway / ciliary transition zone / limb development / receptor clustering / Bergmann glial cell differentiation / cilium assembly / photoreceptor outer segment / axoneme / Hedgehog 'off' state / intercellular bridge / ciliary tip / cellular response to leukemia inhibitory factor / negative regulation of smoothened signaling pathway / sperm end piece / centriole / neural tube closure / centriolar satellite / cell morphogenesis / mitotic spindle / positive regulation of canonical Wnt signaling pathway / sperm principal piece / heart development / microtubule cytoskeleton / protein-containing complex assembly / sperm midpiece / nuclear membrane / in utero embryonic development / cytoskeleton / intracellular signal transduction / cilium / ciliary basal body / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / centrosome / mitochondrion / nucleoplasm / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
IFT144, first zinc finger domain / Intraflagellar transport protein 43 / Intraflagellar transport protein 43 / IFT122, C-terminal zinc ribbon domain / : / IFT122, zinc ribbon domain / Tetratricopeptide repeat protein 21A/21B / : / : / : ...IFT144, first zinc finger domain / Intraflagellar transport protein 43 / Intraflagellar transport protein 43 / IFT122, C-terminal zinc ribbon domain / : / IFT122, zinc ribbon domain / Tetratricopeptide repeat protein 21A/21B / : / : / : / : / : / Tetratricopeptide repeat protein 21 ARM repeat / Tetratricopeptide repeat protein 21 second ARM domain / Tetratricopeptide repeat protein 21 N-terminal ARM repeat / Tetratricopeptide repeat protein 21 C-terminal ARM domain / TT21 fifth ARM repeats domain / Tetratricopeptide repeat protein 21 forth ARM domain / WD repeat protein 35 / WDR19, WD40 repeat / WD repeat-containing protein 19/dyf-2 / : / : / : / : / : / WDR19 second beta-propeller / IFT140 first beta-propeller / IFT140 second beta-propeller / WDR19 first beta-propeller / WDR35 second beta-propeller / IF140 C-terminal TPR domain / WDR35/TULP4 N-terminal / WD repeat-containing protein 35, TPR repeats / : / : / IFT121, second zinc finger domain / IF140/IFT172 TPR domain / : / IFT80/172/WDR35/WDR19 TPR domain / Intraflagellar transport protein 122 homolog / : / : / : / IFT122 second beta-propeller / IFT122 first beta-propeller / IFT122, TPR domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / 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
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water00
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
Has protein modificationY

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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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