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Yorodumi- PDB-7fif: Cryo-EM structure of the hedgehog release protein Disp from water... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7fif | |||||||||||||||||||||
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Title | Cryo-EM structure of the hedgehog release protein Disp from water bear (Hypsibius dujardini) | |||||||||||||||||||||
Components | Protein dispatched-like protein 1 | |||||||||||||||||||||
Keywords | MEMBRANE PROTEIN / cryo-EM / Dispatched / Hedgehog release / Hedgehog signaling / setrol sensing domain / water bear | |||||||||||||||||||||
Function / homology | Membrane transport protein MMPL domain / MMPL family / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain / membrane => GO:0016020 / plasma membrane / Protein dispatched-like protein 1 Function and homology information | |||||||||||||||||||||
Biological species | Hypsibius dujardini (invertebrata) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 Å | |||||||||||||||||||||
Authors | Luo, Y. / Wan, G. / Wang, Q. / Zhao, Y. / Cong, Y. / Li, D. | |||||||||||||||||||||
Funding support | China, 6items
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Citation | Journal: Front Mol Biosci / Year: 2021 Title: Architecture of Dispatched, a Transmembrane Protein Responsible for Hedgehog Release. Authors: Yitian Luo / Guoyue Wan / Xuan Zhou / Qiuwen Wang / Yunbin Zhang / Juan Bao / Yao Cong / Yun Zhao / Dianfan Li / Abstract: The evolutionarily conserved Hedgehog (Hh) signaling pathway is crucial for programmed cell differentiation and proliferation. Dispatched (Disp) is a 12-transmembrane protein that plays a critical ...The evolutionarily conserved Hedgehog (Hh) signaling pathway is crucial for programmed cell differentiation and proliferation. Dispatched (Disp) is a 12-transmembrane protein that plays a critical role in the Hedgehog (Hh) signaling pathway by releasing the dually lipidated ligand HhN from the membrane, a prerequisite step to the downstream signaling cascade. In this study, we focus on the Disp from water bear, a primitive animal known as the most indestructible on Earth. Using a zebrafish model, we show that the water bear homolog possesses the function of Disp. We have solved its structure to a 6.5-Å resolution using single-particle cryogenic electron microscopy. Consistent with the evolutional conservation of the pathway, the water bear Disp structure is overall similar to the previously reported structures of the fruit fly and human homologs. Although not revealing much detail at this resolution, the water bear Disp shows a different conformation compared to published structures, suggesting that they represent different functional snapshots. | |||||||||||||||||||||
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 | 7fif.cif.gz | 134.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fif.ent.gz | 83.8 KB | Display | PDB format |
PDBx/mmJSON format | 7fif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fif_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7fif_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7fif_validation.xml.gz | 29.5 KB | Display | |
Data in CIF | 7fif_validation.cif.gz | 46.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/7fif ftp://data.pdbj.org/pub/pdb/validation_reports/fi/7fif | HTTPS FTP |
-Related structure data
Related structure data | 31595MC 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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1 |
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-Components
#1: Protein | Mass: 124943.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hypsibius dujardini (invertebrata) / Gene: BV898_06340 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: A0A1W0WWK2 |
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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: Dispatched / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 130 kDa/nm / Experimental value: YES | |||||||||||||||||||||||||
Source (natural) | Organism: Hypsibius dujardini (invertebrata) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 3 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 R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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 magnification: 22500 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 900 nm / Calibrated defocus max: 3000 nm / Cs: 0.01 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 7.6 sec. / Electron dose: 60.8 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 5380 |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62850 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6TBU Accession code: 6TBU / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||
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