Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A5B1 

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

Macromolecule Content

• Total Structure Weight: 73.75 kDa 
• Atom Count: 5796 
• Residue Count: 631 
• Unique protein chains: 2

4M1U

The crystal structure of Stx2 and a disaccharide ligand

• DOI: 10.2210/pdb4M1U/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli O157:H7, Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-08-04 Released: 2013-11-20 
• Deposition Author(s): Yin, J., James, M.N.G., Jacobson, J.M., Kitov, P.I., Bundle, D.R., Mulvey, G., Armstrong, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.192 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 

Literature

The crystal structure of shiga toxin type 2 with bound disaccharide guides the design of a heterobifunctional toxin inhibitor.

Jacobson, J.M., Yin, J., Kitov, P.I., Mulvey, G., Griener, T.P., James, M.N., Armstrong, G., Bundle, D.R.

(2014) J Biol Chem 289: 885-894

• PubMed: 24225957 
• DOI: 10.1074/jbc.M113.518886
• Primary Citation of Related Structures:  
  4M1U


• PubMed Abstract: 
  

Shiga toxin type 2 (Stx2a) is clinically most closely associated with enterohemorrhagic E. coli O157:H7-mediated hemorrhagic colitis that sometimes progresses to hemolytic-uremic syndrome. The ability to express the toxin has been acquired by other Escherichia coli strains, and outbreaks of food poisoning have caused significant mortality rates as, for example, in the 2011 outbreak in northern Germany. Stx2a, an AB5 toxin, gains entry into human cells via the glycosphingolipid receptor Gb3. We have determined the first crystal structure of a disaccharide analog of Gb3 bound to the B5 pentamer of Stx2a holotoxin. In this Gb3 analog,-GalNAc replaces the terminal-Gal residue. This co-crystal structure confirms previous inferences that two of the primary binding sites identified in theB5 pentamer of Stx1 are also functional in Stx2a. This knowledge provides a rationale for the synthesis and evaluation of heterobifunctional antagonists for E. coli toxins that target Stx2a. Incorporation of GalNAc Gb3 trisaccharide in a heterobifunctional ligand with an attached pyruvate acetal, a ligand for human amyloid P component, and conjugation to poly[acrylamide-co-(3-azidopropylmethacrylamide)] produced a polymer that neutralized Stx2a in a mouse model of Shigatoxemia.

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Organizational Affiliation: 

From the Department of Chemistry, Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Shiga toxin 2 A-subunit	A	297	Escherichia coli O157:H7	Mutation(s): 0  Gene Names:  ECs1205, stx 2 A-subunit, stx2 A-subunit, stx2A, Z1464, stxA2, E3149_05385, E3153_18140, E3161_19060, E3163_18150, E3164_07970, E3168_18105, E3169_10540, E3170_10240, E3172_17095, E3173_17555, E4U62_17660, E4U67_07870, E4U69_10035, E4U70_18180, E4U72_07905, E4U74_18105, E4U77_07915, E4U80_18420, E4U81_07860, E4U90_07940, ECs_1205, EVY27_08270 EC: 3.2.2.22
Find proteins for Q7DI68 (Escherichia coli O157:H7) Explore Q7DI68  Go to UniProtKB:  Q7DI68

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:  stx2b, stx2dB, stx2vB, stxB2, stxII, vtx2B, stx2B, stx2B_2, BvCmsHHP019_02074, BvCmsNSP072_02053, BvCmsOUP014_04264, C9098_23370, C9Z37_23105, C9Z78_24425, D6004_26885, D7K33_26370, D9X77_26970, DAH30_25515, DM155_24460, DNR35_15450, EBM08_12130, F7F11_25580, HW43_14770, UN91_26180
Find proteins for Q7DJJ2 (Escherichia coli) Explore Q7DJJ2  Go to UniProtKB:  Q7DJJ2

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-4)-methyl beta-D-galactopyranoside	G, H	2		N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PS	B, C, D	3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE C8 H11 N O3 S REEBJQTUIJTGAL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.192 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.25	α = 90
b = 146.25	β = 90
c = 60.31	γ = 120

Software Package:

Software Name	Purpose
MxDC	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-08-04 
• Released Date: 2013-11-20 
Deposition Author(s): Yin, J., James, M.N.G., Jacobson, J.M., Kitov, P.I., Bundle, D.R., Mulvey, G., Armstrong, G.

Revision History 

• Version 1.0: 2013-11-20
  Type: Initial release
  
• Version 1.1: 2013-12-04
  Changes: Database references
• Version 1.2: 2014-02-19
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary