6KRY | pdb_00006kry

Structure of staphylococcal enterotoxin SEN

• PDB DOI: https://doi.org/10.2210/pdb6KRY/pdb

• Classification: ALLERGEN
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-08-22 Released: 2019-12-04 
• Deposition Author(s): Han, Z., Zeng, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.207 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Literature

Structure of Staphylococcal Enterotoxin N: Implications for Binding Properties to Its Cellular Proteins.

Zeng, C., Liu, Z., Han, Z.

(2019) Int J Mol Sci 20

• PubMed: 31775346 
• DOI: https://doi.org/10.3390/ijms20235921
• Primary Citation Related Structures: 
  6KRY


• PubMed Abstract: 
  

  Staphylococcus aureus strains produce a unique family of immunostimulatory exotoxins termed as bacterial superantigens (SAgs), which cross-link major histocompatibility complex class II (MHC II) molecule and T-cell receptor (TCR) to stimulate large numbers of T cells at extremely low concentrations. SAgs are associated with food poisoning and toxic shock syndrome. To date, 26 genetically distinct staphylococcal SAgs have been reported. This study reports the first X-ray structure of newly characterized staphylococcal enterotoxin N (SEN). SEN possesses the classical two domain architecture that includes an N-terminal oligonucleotide-binding fold and a C-terminal β-grasp domain. Amino acid and structure alignments revealed that several critical amino acids that are proposed to be responsible for MHC II and TCR molecule engagements are variable in SEN, suggesting that SEN may adopt a different binding mode to its cellular receptors. This work helps better understand the mechanisms of action of SAgs.

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Organizational Affiliation: 
• College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China.
Hubei Province Fresh Food Engineering Research Center, Wuhan Polytechnic University, Wuhan 430023, China.
Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430064, China.
College of Life Sciences, Wuhan University, Wuhan 430072, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 26.15 kDa 
• Atom Count: 1,992 
• Modeled Residue Count: 224 
• Deposited Residue Count: 227 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enterotoxin SEN variant	A	227	Staphylococcus aureus	Mutation(s): 0  Gene Names: sen, ERS072840_00070, NCTC7878_02454
UniProt
Find proteins for Q6YCN3 (Staphylococcus aureus) Explore Q6YCN3  Go to UniProtKB:  Q6YCN3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.207 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42	α = 90
b = 64.42	β = 110.03
c = 50.14	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-12-04 
Deposition Author(s): Han, Z., Zeng, C.

Revision History  

• Version 1.0: 2019-12-04
  Type: Initial release
  
• Version 1.1: 2019-12-11
  Changes: Database references
• Version 1.2: 2020-05-13
  Changes: Structure summary
• Version 1.3: 2024-03-27
  Changes: Data collection, Database references