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Yorodumi- PDB-7vnn: Complex structure of Clostridioides difficile enzymatic component... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vnn | |||||||||
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Title | Complex structure of Clostridioides difficile enzymatic component (CDTa) and binding component (CDTb) pore with long stem | |||||||||
Components |
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Keywords | TOXIN / Complex / Translocation / Oligomer / Unfoldase | |||||||||
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: 2.64 Å | |||||||||
Authors | Yamada, T. / Kawamoto, A. / Yoshida, T. / Sato, Y. / Kato, T. / Tsuge, H. | |||||||||
Funding support | Japan, 2items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vnn.cif.gz | 831.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vnn.ent.gz | 695.8 KB | Display | PDB format |
PDBx/mmJSON format | 7vnn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vnn_validation.pdf.gz | 828.4 KB | Display | wwPDB validaton report |
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Full document | 7vnn_full_validation.pdf.gz | 865.3 KB | Display | |
Data in XML | 7vnn_validation.xml.gz | 125.1 KB | Display | |
Data in CIF | 7vnn_validation.cif.gz | 194.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vn/7vnn ftp://data.pdbj.org/pub/pdb/validation_reports/vn/7vnn | HTTPS FTP |
-Related structure data
Related structure data | 32043MC 7vnjC 7yvqC 7yvsC 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: 75657.141 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: cdtB / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A8DS70 #2: Protein | | Mass: 49420.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: cdtA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F5B5W8 #3: Chemical | ChemComp-CA / Has ligand of interest | Y | |
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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
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.58 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 | 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 defocus max: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Average exposure time: 3.36 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11284 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 735102 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83061 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building |
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