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Yorodumi- PDB-8qeo: cryo-EM structure complex of Frizzled-7 and Clostridioides diffic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qeo | ||||||||||||||||||||||||||||||||||||
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Title | cryo-EM structure complex of Frizzled-7 and Clostridioides difficile toxin B | ||||||||||||||||||||||||||||||||||||
Components |
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Keywords | TOXIN / micriobiology / class F G protein-coupled receptors / CROP dynamics | ||||||||||||||||||||||||||||||||||||
Function / homology | Function and homology information negative regulation of ectodermal cell fate specification / negative regulation of cardiac muscle cell differentiation / mesenchymal to epithelial transition / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / Wnt receptor activity / somatic stem cell division / non-canonical Wnt signaling pathway / positive regulation of epithelial cell proliferation involved in wound healing / Wnt-protein binding / glucosyltransferase activity ...negative regulation of ectodermal cell fate specification / negative regulation of cardiac muscle cell differentiation / mesenchymal to epithelial transition / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / Wnt receptor activity / somatic stem cell division / non-canonical Wnt signaling pathway / positive regulation of epithelial cell proliferation involved in wound healing / Wnt-protein binding / glucosyltransferase activity / WNT5:FZD7-mediated leishmania damping / frizzled binding / PCP/CE pathway / Class B/2 (Secretin family receptors) / regulation of canonical Wnt signaling pathway / negative regulation of cell-substrate adhesion / Wnt signaling pathway, planar cell polarity pathway / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / stem cell population maintenance / canonical Wnt signaling pathway / cellular response to retinoic acid / positive regulation of phosphorylation / cysteine-type peptidase activity / phosphatidylinositol-4,5-bisphosphate binding / substrate adhesion-dependent cell spreading / host cell endosome membrane / Asymmetric localization of PCP proteins / PDZ domain binding / G protein-coupled receptor activity / positive regulation of JNK cascade / neuron differentiation / recycling endosome membrane / toxin activity / T cell differentiation in thymus / positive regulation of MAPK cascade / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / intracellular membrane-bounded organelle / lipid binding / regulation of DNA-templated transcription / host cell plasma membrane / positive regulation of DNA-templated transcription / proteolysis / extracellular region / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||||||||||||||||||||||||||
Biological species | Clostridioides difficile (bacteria) Homo sapiens (human) | ||||||||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 Å | ||||||||||||||||||||||||||||||||||||
Authors | Kinsolving, J. / Bous, J. | ||||||||||||||||||||||||||||||||||||
Funding support | Sweden, Denmark, 11items
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Citation | Journal: Cell Rep / Year: 2024 Title: Structural and functional insight into the interaction of Clostridioides difficile toxin B and FZD. Authors: Julia Kinsolving / Julien Bous / Pawel Kozielewicz / Sara Košenina / Rawan Shekhani / Lukas Grätz / Geoffrey Masuyer / Yuankai Wang / Pål Stenmark / Min Dong / Gunnar Schulte / Abstract: The G protein-coupled receptors of the Frizzled (FZD) family, in particular FZD, are receptors that are exploited by Clostridioides difficile toxin B (TcdB), the major virulence factor responsible ...The G protein-coupled receptors of the Frizzled (FZD) family, in particular FZD, are receptors that are exploited by Clostridioides difficile toxin B (TcdB), the major virulence factor responsible for pathogenesis associated with Clostridioides difficile infection. We employ a live-cell assay examining the affinity between full-length FZDs and TcdB. Moreover, we present cryoelectron microscopy structures of TcdB alone and in complex with full-length FZD, which reveal that large structural rearrangements of the combined repetitive polypeptide domain are required for interaction with FZDs and other TcdB receptors, constituting a first step for receptor recognition. Furthermore, we show that bezlotoxumab, an FDA-approved monoclonal antibody to treat Clostridioides difficile infection, favors the apo-TcdB structure and thus disrupts binding with FZD. The dynamic transition between the two conformations of TcdB also governs the stability of the pore-forming region. Thus, our work provides structural and functional insight into how conformational dynamics of TcdB determine receptor binding. | ||||||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qeo.cif.gz | 474 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qeo.ent.gz | 364.6 KB | Display | PDB format |
PDBx/mmJSON format | 8qeo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/8qeo ftp://data.pdbj.org/pub/pdb/validation_reports/qe/8qeo | HTTPS FTP |
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-Related structure data
Related structure data | 18374MC 8qenC C: citing same article (ref.) M: map data used to model this data |
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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
#1: Protein | Mass: 273551.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: tcdB / Plasmid: pHis22 / Production host: Priestia megaterium DSM 319 (bacteria) / References: UniProt: P18177 |
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#2: Protein | Mass: 67460.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FZD7 / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75084 |
#3: Chemical | ChemComp-ZN / |
Has ligand of interest | Y |
-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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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 Details: 100 mM TRIS-HCl pH 7.5 200 mM NaCl 0.002% LMNG 0.0002% CHS 0.0002% GDN | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.272 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 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 / Calibrated magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 3 sec. / Electron dose: 50.453 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 17269 Details: Images collected in super-resolution mode, faster acquisition mode, with 4 exposures per hole |
EM imaging optics | Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 5240176 | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 151385 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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