Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 51.24 kDa 
• Atom Count: 4,306 
• Modelled Residue Count: 434 
• Deposited Residue Count: 434 
• Unique protein chains: 1

 2NTT

Crystal Structure of SEK

• PDB DOI:  https://doi.org/10.2210/pdb2NTT/pdb

• Classification: TOXIN
• Organism(s): Staphylococcus aureus subsp. aureus COL
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-11-08 Released: 2007-06-26 
• Deposition Author(s): Gunther, S., Varma, A.K., Moza, B., Sundberg, E.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.202 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

Literature

A novel loop domain in superantigens extends their T cell receptor recognition site

Gunther, S., Varma, A.K., Moza, B., Kasper, K.J., Wyatt, A.W., Zhu, P., Rahman, A.K., Li, Y., Mariuzza, R.A., McCormick, J.K., Sundberg, E.J.

(2007) J Mol Biol 371: 210-221

• PubMed: 17560605 
• DOI: https://doi.org/10.1016/j.jmb.2007.05.038
• Primary Citation of Related Structures:  
  2NTS, 2NTT


• PubMed Abstract: 
  

Superantigens (SAGs) interact with host immune receptors to induce a massive release of inflammatory cytokines that can lead to toxic shock syndrome and death. Bacterial SAGs can be classified into five distinct evolutionary groups. Group V SAGs are characterized by the alpha3-beta8 loop, a unique approximately 15 amino acid residue extension that is required for optimal T cell activation. Here, we report the X-ray crystal structures of the group V SAG staphylococcal enterotoxin K (SEK) alone and in complex with the TCR hVbeta5.1 domain. SEK adopts a unique TCR binding orientation relative to other SAG-TCR complexes, which results in the alpha3-beta8 loop contacting the apical loop of framework region 4, thereby extending the known TCR recognition site of SAGs. These interactions are absolutely required for TCR binding and T cell activation by SEK, and dictate the TCR Vbeta domain specificity of SEK and other group V SAGs.

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Organizational Affiliation: 

Boston Biomedical Research Institute, Watertown, MA 02472, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Staphylococcal enterotoxin K	A, B	217	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0  Gene Names: sek
UniProt
Find proteins for Q93CC5 (Staphylococcus aureus) Explore Q93CC5  Go to UniProtKB:  Q93CC5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 0.202 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.774	α = 90
b = 45.79	β = 90.02
c = 90.696	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-26 
Deposition Author(s): Gunther, S., Varma, A.K., Moza, B., Sundberg, E.J.

Revision History  

• Version 1.0: 2007-06-26
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance