7VHC | pdb_00007vhc

Crystal structure of the STX2a complexed with AR4A peptide

• PDB DOI: https://doi.org/10.2210/pdb7VHC/pdb

• Classification: TOXIN
• Organism(s): Escherichia coli, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-09-22 Released: 2022-07-20 
• Deposition Author(s): Senda, M., Takahashi, M., Nishikawa, K., Senda, T.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.195 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

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

• PubMed: 35794188 
• DOI: https://doi.org/10.1038/s41598-022-15316-1
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Molecular Life Sciences, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan.
Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Ibaraki, Japan.
Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
Transborder Medical Research Center, University of Tsukuba, Ibaraki, Japan.
Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan. [e-mail].
Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Ibaraki, Japan. [e-mail].
Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University of Advanced Studies (Soken-dai), Ibaraki, Japan. [e-mail].
Department of Molecular Life Sciences, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A5B1C1 Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Homo 5-mer - A5 

Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 73.94 kDa 
• Atom Count: 5,530 
• Modeled Residue Count: 637 
• Deposited Residue Count: 654 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
rRNA N-glycosylase	A	297	Escherichia coli	Mutation(s): 0  Gene Names: stx2a EC: 3.2.2.22
UniProt
Find proteins for Q8XBV2 (Escherichia coli) Explore Q8XBV2  Go to UniProtKB:  Q8XBV2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Shiga toxin 2 B subunit	B, C, D, E, F	70	Escherichia coli	Mutation(s): 0  Gene Names: stxII, stx2B, stx2B_2, stx2dB, stx2vB, stxB2, vtx2B
UniProt
Find proteins for Q7DJJ2 (Escherichia coli) Explore Q7DJJ2  Go to UniProtKB:  Q7DJJ2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
inhibitor peptide, ALA-ARG-ARG-ARG-ARG-ALA	G	7	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PS	H [auth B], I [auth C], J [auth D], K [auth F]	3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE C8 H11 N O3 S REEBJQTUIJTGAL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.195 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.226	α = 90
b = 146.226	β = 90
c = 60.205	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-07-20 
Deposition Author(s): Senda, M., Takahashi, M., Nishikawa, K., Senda, T.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP20am0101071

Revision History  

• Version 1.0: 2022-07-20
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary