+Open data
-Basic information
Entry | Database: PDB / ID: 8f5o | |||||||||
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Title | Structure of Leishmania tarentolae IFT-A (state 1) | |||||||||
Components |
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Keywords | PROTEIN TRANSPORT / Cilia / IFT | |||||||||
Function / homology | Function and homology information intraciliary transport particle A / intraciliary retrograde transport / intraciliary transport / non-motile cilium assembly / protein localization to cilium / non-motile cilium / motile cilium / axoneme / cilium assembly / ciliary basal body / cilium Similarity search - Function | |||||||||
Biological species | Leishmania tarentolae (eukaryote) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Zhou, H. / Brown, A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Cell / Year: 2022 Title: Mechanism of IFT-A polymerization into trains for ciliary transport. Authors: Shimi Meleppattu / Haixia Zhou / Jin Dai / Miao Gui / Alan Brown / Abstract: Intraflagellar transport (IFT) is the highly conserved process by which proteins are transported along ciliary microtubules by a train-like polymeric assembly of IFT-A and IFT-B complexes. IFT-A is ...Intraflagellar transport (IFT) is the highly conserved process by which proteins are transported along ciliary microtubules by a train-like polymeric assembly of IFT-A and IFT-B complexes. IFT-A is sandwiched between IFT-B and the ciliary membrane, consistent with its putative role in transporting transmembrane and membrane-associated cargoes. Here, we have used single-particle analysis electron cryomicroscopy (cryo-EM) to determine structures of native IFT-A complexes. We show that subcomplex rearrangements enable IFT-A to polymerize laterally on anterograde IFT trains, revealing a cooperative assembly mechanism. Surprisingly, we discover that binding of IFT-A to IFT-B shields the preferred lipid-binding interface from the ciliary membrane but orients an interconnected network of β-propeller domains with the capacity to accommodate diverse cargoes toward the ciliary membrane. This work provides a mechanistic basis for understanding IFT-train assembly and cargo interactions. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f5o.cif.gz | 999.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f5o.ent.gz | 791.2 KB | Display | PDB format |
PDBx/mmJSON format | 8f5o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/8f5o ftp://data.pdbj.org/pub/pdb/validation_reports/f5/8f5o | HTTPS FTP |
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-Related structure data
Related structure data | 28866MC 8f5pC 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
-Intraflagellar transport protein ... , 2 types, 2 molecules BC
#1: Protein | Mass: 139246.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KAU8 |
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#2: Protein | Mass: 144971.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KU89 |
-WD REPEATS REGION domain-containing ... , 2 types, 2 molecules EF
#3: Protein | Mass: 182580.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KQ11 |
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#5: Protein | Mass: 152393.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KHB7 |
-Protein , 2 types, 2 molecules AD
#4: Protein | Mass: 38742.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KKJ7 |
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#6: Protein | Mass: 180805.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640K949 |
-Non-polymers , 1 types, 4 molecules
#7: Chemical | ChemComp-ZN / |
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-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 | Name: IFT-A / Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL | ||||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Leishmania tarentolae (eukaryote) | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 57.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 239280 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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