7D6R

Crystal structure of the Stx2a complexed with MMA betaAla peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

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Literature

Identification of a peptide motif that potently inhibits two functionally distinct subunits of Shiga toxin.

Watanabe-Takahashi, M.Tamada, M.Senda, M.Hibino, M.Shimizu, E.Okuta, A.Miyazawa, A.Senda, T.Nishikawa, K.

(2021) Commun Biol 4: 538-538

  • DOI: 10.1038/s42003-021-02068-3
  • Primary Citation of Related Structures:  
    7D6Q, 7D6R

  • PubMed Abstract: 
  • Shiga toxin (Stx) is a major virulence factor of enterohemorrhagic Escherichia coli, which causes fatal systemic complications. Here, we identified a tetravalent peptide that inhibited Stx by targeting its receptor-binding, B-subunit pentamer through a multivalent interaction ...

    Shiga toxin (Stx) is a major virulence factor of enterohemorrhagic Escherichia coli, which causes fatal systemic complications. Here, we identified a tetravalent peptide that inhibited Stx by targeting its receptor-binding, B-subunit pentamer through a multivalent interaction. A monomeric peptide with the same motif, however, did not bind to the B-subunit pentamer. Instead, the monomer inhibited cytotoxicity with remarkable potency by binding to the catalytic A-subunit. An X-ray crystal structure analysis to 1.6 Å resolution revealed that the monomeric peptide fully occupied the catalytic cavity, interacting with Glu167 and Arg170, both of which are essential for catalytic activity. Thus, the peptide motif demonstrated potent inhibition of two functionally distinct subunits of Stx.


    Organizational Affiliation

    Department of Molecular Life Sciences, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto, Japan. knishika@mail.doshisha.ac.jp.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
rRNA N-glycosylaseA297Escherichia coliMutation(s): 0 
Gene Names: 
EC: 3.2.2.22
UniProt
Find proteins for Q8XBV2 (Escherichia coli)
Explore Q8XBV2 
Go to UniProtKB:  Q8XBV2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8XBV2
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Shiga toxin 2 B subunitB, C, D, E, F70Escherichia coliMutation(s): 0 
Gene Names: 
UniProt
Find proteins for Q7DJJ2 (Escherichia coli)
Explore Q7DJJ2 
Go to UniProtKB:  Q7DJJ2
Entity Groups  
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UniProt GroupQ7DJJ2
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MMA betaAla peptideG11Escherichia coliMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PS
Query on 1PS

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.489α = 90
b = 146.489β = 90
c = 60.162γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata 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)JapanJP19am0101001

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-14
    Type: Initial release
  • Version 1.1: 2021-05-26
    Changes: Database references