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Yorodumi- PDB-6klw: Complex structure of Iota toxin enzymatic component (Ia) and bind... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6klw | |||||||||
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Title | Complex structure of Iota toxin enzymatic component (Ia) and binding component (Ib) pore with long stem | |||||||||
Components |
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Keywords | TOXIN / Bacterial binary toxin / Protein translocation channel / ADP-ribosylation | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Clostridium perfringens (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Yoshida, T. / Yamada, T. / Kawamoto, A. / Mitsuoka, K. / Iwasaki, K. / Tsuge, H. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Nat Struct Mol Biol / Year: 2020 Title: Cryo-EM structures reveal translocational unfolding in the clostridial binary iota toxin complex. Authors: Tomohito Yamada / Toru Yoshida / Akihiro Kawamoto / Kaoru Mitsuoka / Kenji Iwasaki / Hideaki Tsuge / Abstract: The iota toxin produced by Clostridium perfringens type E is a binary toxin comprising two independent polypeptides: Ia, an ADP-ribosyltransferase, and Ib, which is involved in cell binding and ...The iota toxin produced by Clostridium perfringens type E is a binary toxin comprising two independent polypeptides: Ia, an ADP-ribosyltransferase, and Ib, which is involved in cell binding and translocation of Ia across the cell membrane. Here we report cryo-EM structures of the translocation channel Ib-pore and its complex with Ia. The high-resolution Ib-pore structure demonstrates a similar structural framework to that of the catalytic ϕ-clamp of the anthrax protective antigen pore. However, the Ia-bound Ib-pore structure shows a unique binding mode of Ia: one Ia binds to the Ib-pore, and the Ia amino-terminal domain forms multiple weak interactions with two additional Ib-pore constriction sites. Furthermore, Ib-binding induces tilting and partial unfolding of the Ia N-terminal α-helix, permitting its extension to the ϕ-clamp gate. This new mechanism of N-terminal unfolding is crucial for protein translocation. | |||||||||
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 | 6klw.cif.gz | 572.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6klw.ent.gz | 461.4 KB | Display | PDB format |
PDBx/mmJSON format | 6klw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6klw_validation.pdf.gz | 790.2 KB | Display | wwPDB validaton report |
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Full document | 6klw_full_validation.pdf.gz | 815.3 KB | Display | |
Data in XML | 6klw_validation.xml.gz | 86.6 KB | Display | |
Data in CIF | 6klw_validation.cif.gz | 131.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/6klw ftp://data.pdbj.org/pub/pdb/validation_reports/kl/6klw | HTTPS FTP |
-Related structure data
Related structure data | 0720MC 0713C 0721C 6kloC 6klxC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10483 (Title: ISWI-NCP complex in the ADP-bound state / Data size: 36.2 Data #1: The ISWI-NCP complex in the ADP-bound state [picked particles - multiframe - processed]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 74378.820 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (bacteria) / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami / References: UniProt: Q46221 #2: Protein | | Mass: 48061.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (bacteria) / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q46220 #3: Chemical | ChemComp-CA / Has ligand of interest | N | |
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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: Complex structure of Iota toxin enzymatic component (Ia) and binding component (Ib) pore with long stem Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.57 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Clostridium perfringens (bacteria) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.48 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 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 / Nominal magnification: 59000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 78.9 K / Temperature (min): 78.9 K |
Image recording | Average exposure time: 84.09 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2151 |
EM imaging optics | Spherical aberration corrector: Microscope was modified with a Cs corrector |
Image scans | Width: 4096 / Height: 4096 |
-Processing
Software | Name: PHENIX / Version: (1.15.2_3472: phenix.real_space_refine) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 871264 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62940 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 29 / Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 3J9C Accession code: 3J9C / Source name: PDB / Type: experimental model |