5XZ0 | pdb_00005xz0

Staphylococcal Enterotoxin B (SEB) mutant S19 - N23A, Y90A, R110A and F177A

• PDB DOI: https://doi.org/10.2210/pdb5XZ0/pdb

• Classification: TOXIN
• Organism(s): Staphylococcus aureus subsp. aureus COL
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-07-11 Released: 2017-11-01 
• Deposition Author(s): Jeong, W.H., Song, D.H., Hur, G.H., Jeong, S.T.
• Funding Organization(s): Agency for Defense Development

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.243 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Models: experimental

Literature

Structure of the staphylococcal enterotoxin B vaccine candidate S19 showing eliminated superantigen activity

Jeong, W.H., Song, D.H., Hur, G.H., Jeong, S.T.

(2017) Acta Crystallogr F Struct Biol Commun 73: 595-600

• PubMed: 29095152 
• DOI: https://doi.org/10.1107/S2053230X17014844
• Primary Citation Related Structures: 
  5XZ0


• PubMed Abstract: 
  

  Four mutations (N23A, Y90A, R110A and F177A) were introduced into S19, a vaccine candidate for staphylococcal enterotoxin B (SEB), resulting in a lower binding affinity towards the T-cell receptor beta chain (TCB) and reducing its superantigen activity. The structure of S19 was solved and was superposed on the native or complex structure of SEB. In the superposition model, mutations that were introduced seemed to reduce the number of hydrogen bonds at the SEB-TCB interface. S19 also displayed an unexpected structural change around the flexible-loop region owing to the Y90A mutation. This local structural change provided evidence that the mutated form of S19 could have a lower affinity for major histocompatibility complex (MHC) class II than wild-type SEB.

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Organizational Affiliation: 
• The 5th R&D Institute, Agency for Defense Development, Yuseong PO Box 35, Yuseong-gu, Daejeon 34188, Republic of Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 55.19 kDa 
• Atom Count: 3,702 
• Modeled Residue Count: 444 
• Deposited Residue Count: 470 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Staphylococcal enterotoxin B	A, B	235	Staphylococcus aureus subsp. aureus COL	Mutation(s): 4  Gene Names: seb, SACOL0907
UniProt
Find proteins for A0A0H2WZB2 (Staphylococcus aureus (strain COL)) Explore A0A0H2WZB2  Go to UniProtKB:  A0A0H2WZB2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.243 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.565	α = 90
b = 174.63	β = 90
c = 48.769	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-11-01 
Deposition Author(s): Jeong, W.H., Song, D.H., Hur, G.H., Jeong, S.T.

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Funding Organization	Location	Grant Number
Agency for Defense Development	Korea, Republic Of	07-203-603-005

Revision History  

• Version 1.0: 2017-11-01
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary