5XZ0

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/10.1107/S2053230X17014844
  • Primary Citation of 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Staphylococcal enterotoxin B
A, B
235Staphylococcus aureus subsp. aureus COLMutation(s): 4 
Gene Names: sebSACOL0907
UniProt
Find proteins for A0A0H2WZB2 (Staphylococcus aureus (strain COL))
Explore A0A0H2WZB2 
Go to UniProtKB:  A0A0H2WZB2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2WZB2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.208 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.565α = 90
b = 174.63β = 90
c = 48.769γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agency for Defense DevelopmentKorea, Republic Of07-203-603-005

Revision History  (Full details and data files)

  • 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