7VHC

Crystal structure of the STX2a complexed with AR4A peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A unique peptide-based pharmacophore identifies an inhibitory compound against the A-subunit of Shiga toxin.

Watanabe-Takahashi, M.Senda, M.Yoshino, R.Hibino, M.Hama, S.Terada, T.Shimizu, K.Senda, T.Nishikawa, K.

(2022) Sci Rep 12: 11443-11443

  • DOI: https://doi.org/10.1038/s41598-022-15316-1
  • Primary Citation of Related Structures:  
    7VHC, 7VHD, 7VHE, 7VHF

  • PubMed Abstract: 

    Shiga toxin (Stx), a major virulence factor of enterohemorrhagic Escherichia coli (EHEC), can cause fatal systemic complications. Recently, we identified a potent inhibitory peptide that binds to the catalytic A-subunit of Stx. Here, using biochemical structural analysis and X-ray crystallography, we determined a minimal essential peptide motif that occupies the catalytic cavity and is required for binding to the A-subunit of Stx2a, a highly virulent Stx subtype. Molecular dynamics simulations also identified the same motif and allowed determination of a unique pharmacophore for A-subunit binding. Notably, a series of synthetic peptides containing the motif efficiently inhibit Stx2a. In addition, pharmacophore screening and subsequent docking simulations ultimately identified nine Stx2a-interacting molecules out of a chemical compound database consisting of over 7,400,000 molecules. Critically, one of these molecules markedly inhibits Stx2a both in vitro and in vivo, clearly demonstrating the significance of the pharmacophore for identifying therapeutic agents against EHEC infection.


  • Organizational Affiliation

    Department of Molecular Life Sciences, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
rRNA N-glycosylase297Escherichia coliMutation(s): 0 
Gene Names: stx2a
EC: 3.2.2.22
UniProt
Find proteins for Q7DI68 (Escherichia coli O157:H7)
Explore Q7DI68 
Go to UniProtKB:  Q7DI68
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7DI68
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Shiga toxin 2 B subunit
B, C, D, E, F
70Escherichia coliMutation(s): 0 
Gene Names: stxIIstx2Bstx2B_2stx2dBstx2vBstxB2vtx2B
UniProt
Find proteins for A7UQX3 (Escherichia coli O157:H7)
Explore A7UQX3 
Go to UniProtKB:  A7UQX3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7UQX3
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
inhibitor peptide, ALA-ARG-ARG-ARG-ARG-ALA7synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.226α = 90
b = 146.226β = 90
c = 60.205γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP20am0101071

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-20
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description