6X6H

Structure of Shiga toxin 2 with a C-terminal peptide of ribosomal P stalk proteins


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

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This is version 2.1 of the entry. See complete history


Literature

Structural basis for the interaction of Shiga toxin 2a with a C-terminal peptide of ribosomal P stalk proteins.

Rudolph, M.J.Davis, S.A.Tumer, N.E.Li, X.P.

(2020) J Biol Chem 295: 15588-15596

  • DOI: 10.1074/jbc.AC120.015070
  • Primary Citation of Related Structures:  
    6X6H

  • PubMed Abstract: 
  • The principal virulence factor of human pathogenic enterohemorrhagic Escherichia coli is Shiga toxin (Stx). Shiga toxin 2a (Stx2a) is the subtype most commonly associated with severe disease outcomes such as hemorrhagic colitis and hemolytic uremic syndrome ...

    The principal virulence factor of human pathogenic enterohemorrhagic Escherichia coli is Shiga toxin (Stx). Shiga toxin 2a (Stx2a) is the subtype most commonly associated with severe disease outcomes such as hemorrhagic colitis and hemolytic uremic syndrome. The catalytic A1 subunit (Stx2A1) binds to the conserved elongation factor binding C-terminal domain (CTD) of ribosomal P stalk proteins to inhibit translation. Stx2a holotoxin also binds to the CTD of P stalk proteins because the ribosome-binding site is exposed. We show here that Stx2a binds to an 11-mer peptide (P11) mimicking the CTD of P stalk proteins with low micromolar affinity. We cocrystallized Stx2a with P11 and defined their interactions by X-ray crystallography. We found that the last six residues of P11 inserted into a shallow pocket on Stx2A1 and interacted with Arg-172, Arg-176, and Arg-179, which were previously shown to be critical for binding of Stx2A1 to the ribosome. Stx2a formed a distinct P11-binding mode within a different surface pocket relative to ricin toxin A subunit and trichosanthin, suggesting different ribosome recognition mechanisms for each ribosome inactivating protein (RIP). The binding mode of Stx2a to P11 is also conserved among the different Stx subtypes. Furthermore, the P stalk protein CTD is flexible and adopts distinct orientations and interaction modes depending on the structural differences between the RIPs. Structural characterization of the Stx2a-ribosome complex is important for understanding the role of the stalk in toxin recruitment to the sarcin/ricin loop and may provide a new target for inhibitor discovery.


    Organizational Affiliation

    Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA xpli@sebs.rutgers.edu tumer@sebs.rutgers.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
rRNA N-glycosylaseA [auth A1]242Escherichia coliMutation(s): 0 
Gene Names: 
EC: 3.2.2.22
UniProt
Find proteins for A9ZMR8 (Escherichia coli)
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UniProt GroupA9ZMR8
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
rRNA N-glycosylaseB [auth A2]40Escherichia coliMutation(s): 0 
Gene Names: 
EC: 3.2.2.22
UniProt
Find proteins for A9ZMR8 (Escherichia coli)
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UniProt GroupA9ZMR8
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Shiga toxin 2 B subunitC [auth B],
D [auth C],
E [auth D],
F [auth E],
G [auth F]
70Escherichia coliMutation(s): 0 
Gene Names: 
UniProt
Find proteins for Q7DJJ2 (Escherichia coli)
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UniProt GroupQ7DJJ2
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
P11 peptideH [auth P]6Escherichia coliMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.148α = 90
b = 85.226β = 90
c = 98.841γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2020-05-28 
  • Released Date: 2020-09-09 
  • Deposition Author(s): Rudolph, M.J.

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-09
    Type: Initial release
  • Version 2.0: 2020-09-16
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Structure summary
  • Version 2.1: 2020-11-25
    Changes: Database references