+Open data
-Basic information
Entry | Database: PDB / ID: 6tbu | |||||||||
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Title | Structure of Drosophila melanogaster Dispatched | |||||||||
Components | Protein dispatched | |||||||||
Keywords | MEMBRANE PROTEIN / RND transporter / transmembrane domain / ectodomain / cholesteryl hemisuccinate / detergent micelle / digitonin / monomer | |||||||||
Function / homology | Function and homology information Formation and transport of the N-HH ligand / cytoneme / wing disc pattern formation / patched ligand maturation / segment polarity determination / germ cell migration / smoothened signaling pathway / transmembrane transporter activity / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å | |||||||||
Authors | Korkhov, V.M. / Cannac, F. | |||||||||
Funding support | Switzerland, 1items
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Citation | Journal: Sci Adv / Year: 2020 Title: Cryo-EM structure of the Hedgehog release protein Dispatched. Authors: Fabien Cannac / Chao Qi / Julia Falschlunger / George Hausmann / Konrad Basler / Volodymyr M Korkhov / Abstract: The Hedgehog (Hh) signaling pathway controls embryonic development and adult tissue homeostasis in multicellular organisms. In , the pathway is primed by secretion of a dually lipid-modified ...The Hedgehog (Hh) signaling pathway controls embryonic development and adult tissue homeostasis in multicellular organisms. In , the pathway is primed by secretion of a dually lipid-modified morphogen, Hh, a process dependent on a membrane-integral protein Dispatched. Although Dispatched is a critical component of the pathway, the structural basis of its activity has, so far, not been described. Here, we describe a cryo-electron microscopy structure of the Dispatched at 3.2-Å resolution. The ectodomains of Dispatched adopt an open conformation suggestive of a receptor-chaperone role. A three-dimensional reconstruction of Dispatched bound to Hh confirms the ability of Dispatched to bind Hh but using a unique mode distinct from those previously observed in structures of Hh complexes. The structure may represent the state of the complex that precedes shedding of Hh from the surface of the morphogen-releasing cell. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6tbu.cif.gz | 304.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tbu.ent.gz | 252.1 KB | Display | PDB format |
PDBx/mmJSON format | 6tbu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tbu_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6tbu_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6tbu_validation.xml.gz | 40.3 KB | Display | |
Data in CIF | 6tbu_validation.cif.gz | 58.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tb/6tbu ftp://data.pdbj.org/pub/pdb/validation_reports/tb/6tbu | HTTPS FTP |
-Related structure data
Related structure data | 10452MC 6td6C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 139149.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Drosophila melanogaster Dispatched, tagged with a C-terminal 3C-protease cleavage site, YFP and twin-strep tag. Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: disp, CG2019 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9VNJ5 | ||||
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
#3: Chemical | ChemComp-Y01 / #4: Sugar | ChemComp-NAG / | Has ligand of interest | N | |
-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: Drosophila melanogaster protein Dispatched (disp) / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.139 MDa / Experimental value: NO |
Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Source (recombinant) | Organism: Homo sapiens (human) |
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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of real images: 9216 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||
3D reconstruction | Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 286136 / Symmetry type: POINT |