1DYQ | pdb_00001dyq

STAPHYLOCOCCAL ENTEROTOXIN A MUTANT VACCINE

• PDB DOI: https://doi.org/10.2210/pdb1DYQ/pdb

• Classification: ENTEROTOXIN
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2000-02-05 Released: 2001-03-19 
• Deposition Author(s): Krupka, H.I., Segelke, B.W., Rupp, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.236 (Depositor) 
• R-Value Work: 
  0.191 (Depositor), 0.185 (DCC) 

Starting Model: experimental

Literature

Structural Basis for Abrogated Binding between Staphylococcal Enterotoxin a Superantigen Vaccine and Mhc-II?

Krupka, H.I., Segelke, B.W., Ulrich, R., Ringhofer, S., Knapp, M., Rupp, B.

(2002) Protein Sci 11: 642

• PubMed: 11847286 
• DOI: https://doi.org/10.1110/ps.39702
• Primary Citation Related Structures: 
  1DYQ


• PubMed Abstract: 
  

  Staphylococcal enterotoxins (SEs) are superantigenic protein toxins responsible for a number of life-threatening diseases. The X-ray structure of a staphylococcal enterotoxin A (SEA) triple-mutant (L48R, D70R, and Y92A) vaccine reveals a cascade of structural rearrangements located in three loop regions essential for binding the alpha subunit of major histocompatibility complex class II (MHC-II) molecules. A comparison of hypothetical model complexes between SEA and the SEA triple mutant with MHC-II HLA-DR1 clearly shows disruption of key ionic and hydrophobic interactions necessary for forming the complex. Extensive dislocation of the disulfide loop in particular interferes with MHC-IIalpha binding. The triple-mutant structure provides new insights into the loss of superantigenicity and toxicity of an engineered superantigen and provides a basis for further design of enterotoxin vaccines.

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Organizational Affiliation: 
• Lawrence Livermore National Laboratory, Macromolecular Crystallography, Biology and Biotechnology Research Program, University of California, Livermore, California 94551, USA.

Biological Assembly 1  

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

Biological assembly 1 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 27.42 kDa 
• Atom Count: 2,382 
• Modeled Residue Count: 228 
• Deposited Residue Count: 234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enterotoxin type A	A	234	Staphylococcus aureus	Mutation(s): 3  Gene Names: entA
UniProt
Find proteins for P0A0L2 (Staphylococcus aureus) Explore P0A0L2  Go to UniProtKB:  P0A0L2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.236 (Depositor) 
• R-Value Work:  0.191 (Depositor), 0.185 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.048	α = 90
b = 78.652	β = 90
c = 86.374	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-03-19 
Deposition Author(s): Krupka, H.I., Segelke, B.W., Rupp, B.

Revision History  

• Version 1.0: 2001-03-19
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-04-03
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 1.5: 2019-09-25
  Changes: Advisory, Data collection, Database references, Source and taxonomy, Structure summary
• Version 1.6: 2023-12-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.7: 2024-11-13
  Changes: Structure summary