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- EMDB-0608: Reconstruction of CDTb Double Heptamer Long Form using C7 Symmetry -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0608 | |||||||||
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Title | Reconstruction of CDTb Double Heptamer Long Form using C7 Symmetry | |||||||||
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![]() | CDTb
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Function / homology | ![]() protein homooligomerization / ![]() ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Lacy DB / Sheedlo MJ / Anderson DM | |||||||||
Funding support | ![]()
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![]() | ![]() 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. | |||||||||
Validation Report | ![]() ![]() ![]() ![]() | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
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Download
FSC (resolution estimation) |
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Header (meta data in XML format) |
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Images |
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Archive directory |
-Related structure data
Related structure data | ![]() 6o2mCM ![]() 0609C ![]() 0610C ![]() 6o2nC ![]() 6o2oC ![]() 6okrC ![]() 6oksC ![]() 6oktC ![]() 6okuC C: citing same article ( M: atomic model generated by this map |
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Similar-shape strucutres |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.45 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire CDTb
Entire | Name: CDTb / Number of components: 2 |
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-Component #1: protein, CDTb
Protein | Name: CDTb / Recombinant expression: No |
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Source | Species: ![]() ![]() |
Source (engineered) | Expression System: ![]() ![]() ![]() |
-Component #2: protein, ADP-ribosyltransferase binding component
Protein | Name: ADP-ribosyltransferase binding component![]() Number of Copies: 14 / Recombinant expression: No |
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Mass | Theoretical: 98.916828 kDa |
Source | Species: ![]() ![]() |
Source (engineered) | Expression System: ![]() ![]() ![]() |
-Experimental details
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Sample preparation
Specimen | Specimen state: Particle / Method: ![]() |
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Sample solution | pH: 8 |
Support film | unspecified |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 100 % |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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![]() | Microscope: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN![]() |
Lens | Imaging mode: BRIGHT FIELD![]() |
Specimen Holder | Model: OTHER |
Camera | Detector: GATAN K2 SUMMIT (4k x 4k) |
-Image acquisition
Image acquisition | Number of digital images: 4914 |
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Image processing
-Atomic model buiding
Modeling #1 | Refinement space: REAL |
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Output model |