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Yorodumi- EMDB-33188: Complex map of Clostridioides difficile enzymatic component (CDTa... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33188 | |||||||||
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Title | Complex map of Clostridioides difficile enzymatic component (CDTa) and binding component (CDTb) di-heptamer | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Complex / Translocation / Oligomer / Unfoldase / TOXIN | |||||||||
Biological species | Clostridioides difficile (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.19 Å | |||||||||
Authors | Yamada T / Kawamoto A / Yoshida T / Sato Y / Kato T / Tsuge H | |||||||||
Funding support | Japan, 2 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Cryo-EM structures of the translocational binary toxin complex CDTa-bound CDTb-pore from Clostridioides difficile. Authors: Akihiro Kawamoto / Tomohito Yamada / Toru Yoshida / Yusui Sato / Takayuki Kato / Hideaki Tsuge / Abstract: Some bacteria express a binary toxin translocation system, consisting of an enzymatic subunit and translocation pore, that delivers enzymes into host cells through endocytosis. The most clinically ...Some bacteria express a binary toxin translocation system, consisting of an enzymatic subunit and translocation pore, that delivers enzymes into host cells through endocytosis. The most clinically important bacterium with such a system is Clostridioides difficile (formerly Clostridium). The CDTa and CDTb proteins from its system represent important therapeutic targets. CDTb has been proposed to be a di-heptamer, but its physiological heptameric structure has not yet been reported. Here, we report the cryo-EM structure of CDTa bound to the CDTb-pore, which reveals that CDTa binding induces partial unfolding and tilting of the first CDTa α-helix. In the CDTb-pore, an NSS-loop exists in 'in' and 'out' conformations, suggesting its involvement in substrate translocation. Finally, 3D variability analysis revealed CDTa movements from a folded to an unfolded state. These dynamic structural information provide insights into drug design against hypervirulent C. difficile strains. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33188.map.gz | 48.1 MB | EMDB map data format | |
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Header (meta data) | emd-33188-v30.xml emd-33188.xml | 15.6 KB 15.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33188_fsc.xml | 18.9 KB | Display | FSC data file |
Images | emd_33188.png | 104.2 KB | ||
Others | emd_33188_half_map_1.map.gz emd_33188_half_map_2.map.gz | 391.4 MB 391.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33188 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33188 | HTTPS FTP |
-Validation report
Summary document | emd_33188_validation.pdf.gz | 905.6 KB | Display | EMDB validaton report |
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Full document | emd_33188_full_validation.pdf.gz | 905.2 KB | Display | |
Data in XML | emd_33188_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | emd_33188_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33188 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33188 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33188.map.gz / Format: CCP4 / Size: 488.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.88 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_33188_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33188_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : CDTa-bound CDTb-pore (long)
Entire | Name: CDTa-bound CDTb-pore (long) |
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Components |
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-Supramolecule #1: CDTa-bound CDTb-pore (long)
Supramolecule | Name: CDTa-bound CDTb-pore (long) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Clostridioides difficile (bacteria) |
-Supramolecule #2: CDTb di-heptamer
Supramolecule | Name: CDTb di-heptamer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Clostridioides difficile (bacteria) |
-Supramolecule #3: CdtA
Supramolecule | Name: CdtA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.58 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 11284 / Average exposure time: 3.36 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |