6KLX

Pore structure of Iota toxin binding component (Ib)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structures reveal translocational unfolding in the clostridial binary iota toxin complex.

Yamada, T.Yoshida, T.Kawamoto, A.Mitsuoka, K.Iwasaki, K.Tsuge, H.

(2020) Nat Struct Mol Biol 27: 288-296

  • DOI: 10.1038/s41594-020-0388-6
  • Structures With Same Primary Citation

  • PubMed 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 translocation of Ia across the cell membrane. Here we re ...

    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.


    Organizational Affiliation

    Center for Molecular Research in Infectious Diseases, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto, Japan. tsuge@cc.kyoto-su.ac.jp.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Iota toxin component Ib
A, B, C, D, E, F, G
666Clostridium perfringensMutation(s): 0 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Adventitious Membrane Proteins: Beta-sheet Pore-forming Toxins/Attack Complexes
Protein: 
Binary iota toxin complex Ib pore
Find proteins for Q46221 (Clostridium perfringens)
Go to UniProtKB:  Q46221
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download CCD File 
A, B, C, D, E, F, G
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan18K06170
Japan Society for the Promotion of ScienceJapan17K15095

Revision History 

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-03-18
    Changes: Database references
  • Version 1.2: 2020-03-25
    Changes: Database references