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Yorodumi- PDB-8fh3: Human IFT-A complex structures provide molecular insights into ci... -
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-Basic information
Entry | Database: PDB / ID: 8fh3 | ||||||
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Title | Human IFT-A complex structures provide molecular insights into ciliary transport | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / IFT-A complex / TULP3 / cilia | ||||||
Function / homology | Function and homology information negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning / intraciliary transport particle A binding / negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning / smoothened signaling pathway involved in dorsal/ventral neural tube patterning / myotome development / ear morphogenesis / intraciliary anterograde transport / ganglion development / cone photoreceptor outer segment / bronchus morphogenesis ...negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning / intraciliary transport particle A binding / negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning / smoothened signaling pathway involved in dorsal/ventral neural tube patterning / myotome development / ear morphogenesis / intraciliary anterograde transport / ganglion development / cone photoreceptor outer segment / bronchus morphogenesis / digestive system development / intraciliary transport particle A / embryonic heart tube left/right pattern formation / embryonic body morphogenesis / embryonic neurocranium morphogenesis / neural tube patterning / photoreceptor cell outer segment organization / central nervous system neuron differentiation / 9+0 non-motile cilium / 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 brain development / regulation of G protein-coupled receptor signaling pathway / non-motile cilium assembly / protein localization to cilium / regulation of smoothened signaling pathway / embryonic heart tube development / embryonic cranial skeleton morphogenesis / non-motile cilium / nervous system process / embryonic forelimb morphogenesis / motile cilium / determination of left/right symmetry / embryonic limb morphogenesis / limb development / anterior/posterior pattern specification / ciliary base / embryonic digit morphogenesis / receptor clustering / axoneme / photoreceptor outer segment / cilium assembly / Hedgehog 'off' state / negative regulation of smoothened signaling pathway / phosphatidylinositol-4,5-bisphosphate binding / centriole / phosphatidylinositol binding / ciliary basal body / cellular response to leukemia inhibitory factor / neural tube closure / G protein-coupled receptor binding / bone development / brain development / cell morphogenesis / cilium / heart development / protein-containing complex assembly / in utero embryonic development / cytoskeleton / intracellular signal transduction / G protein-coupled receptor signaling pathway / centrosome / regulation of DNA-templated transcription / protein-containing complex binding / nucleolus / enzyme binding / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||
Authors | Jiang, M. / Palicharla, V.R. / Miller, D. / Hwang, S.H. / Zhu, H. / Hixson, P. / Mukhopadhyay, S. / Sun, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fh3.cif.gz | 658.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fh3.ent.gz | 499.8 KB | Display | PDB format |
PDBx/mmJSON format | 8fh3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fh3_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8fh3_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8fh3_validation.xml.gz | 106.4 KB | Display | |
Data in CIF | 8fh3_validation.cif.gz | 161.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/8fh3 ftp://data.pdbj.org/pub/pdb/validation_reports/fh/8fh3 | HTTPS FTP |
-Related structure data
Related structure data | 29078MC 8fgwC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-WD repeat-containing protein ... , 2 types, 2 molecules AC
#1: Protein | 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 |
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#3: Protein | 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 |
-Intraflagellar transport protein ... , 2 types, 2 molecules BE
#2: Protein | 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 |
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#4: Protein | 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 |
-Protein / Non-polymers , 2 types, 5 molecules I
#5: Protein | Mass: 49710.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TULP3, TUBL3 / Production host: Homo sapiens (human) / References: UniProt: O75386 |
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#6: Chemical | ChemComp-ZN / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 | ||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 53.06 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113784 / Symmetry type: POINT |