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Yorodumi- PDB-6oks: CDTb Double Heptamer Long Form Mask 1 Modeled from Cryo-EM Map Re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6oks | |||||||||
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Title | CDTb Double Heptamer Long Form Mask 1 Modeled from Cryo-EM Map Reconstructed using C7 Symmetry | |||||||||
Components | ADP-ribosyltransferase binding component | |||||||||
Keywords | TRANSFERASE / CDTb / Clostridium / Toxin / Binary / difficil | |||||||||
Function / homology | Function and homology information protein homooligomerization / transferase activity / extracellular region / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Clostridioides difficile (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Lacy, D.B. / Sheedlo, M.J. / Anderson, D.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Microbiol / Year: 2020 Title: Structural insights into the transition of Clostridioides difficile binary toxin from prepore to pore. Authors: David M Anderson / Michael J Sheedlo / Jaime L Jensen / D Borden Lacy / Abstract: Clostridioides (formerly Clostridium) difficile is a Gram-positive, spore-forming anaerobe and a leading cause of hospital-acquired infection and gastroenteritis-associated death in US hospitals. The ...Clostridioides (formerly Clostridium) difficile is a Gram-positive, spore-forming anaerobe and a leading cause of hospital-acquired infection and gastroenteritis-associated death in US hospitals. The disease state is usually preceded by disruption of the host microbiome in response to antibiotic treatment and is characterized by mild to severe diarrhoea. C. difficile infection is dependent on the secretion of one or more AB-type toxins: toxin A (TcdA), toxin B (TcdB) and the C. difficile transferase toxin (CDT). Whereas TcdA and TcdB are considered the primary virulence factors, recent studies suggest that CDT increases the severity of C. difficile infection in some of the most problematic clinical strains. To better understand how CDT functions, we used cryo-electron microscopy to define the structure of CDTb, the cell-binding component of CDT. We obtained structures of several oligomeric forms that highlight the conformational changes that enable conversion from a prepore to a β-barrel pore. The structural analysis also reveals a glycan-binding domain and residues involved in binding the host-cell receptor, lipolysis-stimulated lipoprotein receptor. Together, these results provide a framework to understand how CDT functions at the host cell interface. | |||||||||
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 | 6oks.cif.gz | 456.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oks.ent.gz | 276.8 KB | Display | PDB format |
PDBx/mmJSON format | 6oks.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6oks_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6oks_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6oks_validation.xml.gz | 39 KB | Display | |
Data in CIF | 6oks_validation.cif.gz | 64.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/6oks ftp://data.pdbj.org/pub/pdb/validation_reports/ok/6oks | HTTPS FTP |
-Related structure data
Related structure data | 20103MC 0608C 0609C 0610C 6o2mC 6o2nC 6o2oC 6okrC 6oktC 6okuC 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: 98916.828 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: cdtB / Production host: Escherichia coli (E. coli) / References: UniProt: A8DS70 |
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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: CDTb / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Clostridioides difficile (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 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 |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 9.6 sec. / Electron dose: 110.1 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 4914 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13266 / Symmetry type: POINT | |||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |