6U3U | pdb_00006u3u

Crystal Structure of Shiga Toxin 2K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 
    0.225 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural and Functional Characterization of Stx2k, a New Subtype of Shiga Toxin 2.

Hughes, A.C.Zhang, Y.Bai, X.Xiong, Y.Wang, Y.Yang, X.Xu, Q.He, X.

(2019) Microorganisms 8

  • DOI: https://doi.org/10.3390/microorganisms8010004
  • Primary Citation Related Structures: 
    6U3U

  • PubMed Abstract: 

    Shiga toxin (Stx) is the major virulence factor of Shiga toxin-producing Escherichia coli (STEC). Stx evolves rapidly and, as such, new subtypes continue to emerge that challenge the efficacy of existing disease management and surveillance strategies. A new subtype, Stx2k, was recently identified in E. coli isolated from a wide range of sources including diarrheal patients, animals, and raw meats, and was poorly detected by existing immunoassays. In this study, the structure of Stx2kE167Q was determined at 2.29 Å resolution and the conservation of structure with Stx2a was revealed. A novel polyclonal antibody capable of neutralizing Stx2k and an immunoassay, with a 10-fold increase in sensitivity compared to assays using extant antibodies, were developed. Stx2k is less toxic than Stx2a in Vero cell assays but is similar to Stx2a in receptor-binding preference, thermostability, and acid tolerance. Although Stx2k does not appear to be as potent as Stx2a to Vero cells, the wide distribution and blended virulence profiles of the Stx2k-producing strains suggest that horizontal gene transfer through Stx2k-converting phages could result in the emergence of new and highly virulent pathogens. This study provides useful information and tools for early detection and control of Stx2k-producing E. coli , which could reduce public risk of infection by less-known STECs.


  • Organizational Affiliation
    • Western Regional Research Center, United States Department of Agriculture, Agricultural Research Service, 800 Buchanan St., Albany, CA 94710, USA.

Macromolecule Content 

  • Total Structure Weight: 144.54 kDa 
  • Atom Count: 10,054 
  • Modeled Residue Count: 1,266 
  • Deposited Residue Count: 1,294 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Shiga toxin 2K subunit AA [auth B],
G [auth A]
297Escherichia coliMutation(s): 1 
Gene Names: stx2A
EC: 3.2.2.22
UniProt
Find proteins for L0I969 (Escherichia coli)
Explore L0I969 
Go to UniProtKB:  L0I969
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL0I969
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Shiga toxin 2K subunit B70Escherichia coliMutation(s): 0 
Gene Names: vtx2Bstx2Bstx2B_2BvCmsKKP036_03423BvCmsNSP045_04912
UniProt
Find proteins for Q4PS70 (Escherichia coli)
Explore Q4PS70 
Go to UniProtKB:  Q4PS70
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4PS70
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE

Query on EPE



Download:Ideal Coordinates CCD File
M [auth B],
U [auth A]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
T [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
N [auth B]
O [auth B]
P [auth B]
Q [auth C]
R [auth D]
N [auth B],
O [auth B],
P [auth B],
Q [auth C],
R [auth D],
S [auth I],
V [auth J]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free:  0.225 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.178α = 90
b = 157.022β = 94.61
c = 107.407γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United States Department of Agriculture (USDA)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-10-16
    Changes: Structure summary