6RO0

CRYSTAL STRUCTURE OF GENETICALLY DETOXIFIED PERTUSSIS TOXIN GDPT.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Genetically detoxified pertussis toxin displays near identical structure to its wild-type and exhibits robust immunogenicity.

Ausar, S.F.Zhu, S.Duprez, J.Cohen, M.Bertrand, T.Steier, V.Wilson, D.J.Li, S.Sheung, A.Brookes, R.H.Pedyczak, A.Rak, A.Andrew James, D.

(2020) Commun Biol 3: 427-427

  • DOI: https://doi.org/10.1038/s42003-020-01153-3
  • Primary Citation of Related Structures:  
    6RO0

  • PubMed Abstract: 

    The mutant gdPT R9K/E129G is a genetically detoxified variant of the pertussis toxin (PTx) and represents an attractive candidate for the development of improved pertussis vaccines. The impact of the mutations on the overall protein structure and its immunogenicity has remained elusive. Here we present the crystal structure of gdPT and show that it is nearly identical to that of PTx. Hydrogen-deuterium exchange mass spectrometry revealed dynamic changes in the catalytic domain that directly impacted NAD + binding which was confirmed by biolayer interferometry. Distal changes in dynamics were also detected in S2-S5 subunit interactions resulting in tighter packing of B-oligomer corresponding to increased thermal stability. Finally, antigen stimulation of human whole blood, analyzed by a previously unreported mass cytometry assay, indicated broader immunogenicity of gdPT compared to pertussis toxoid. These findings establish a direct link between the conserved structure of gdPT and its ability to generate a robust immune response.


  • Organizational Affiliation

    Bioprocess Research and Development, Sanofi Pasteur Ltd., Toronto, ON, M2R 3T4, Canada.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pertussis toxin subunit 1
A, G
269Bordetella pertussisMutation(s): 2 
Gene Names: ptxA
UniProt
Find proteins for P04977 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251))
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Go to UniProtKB:  P04977
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04977
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Islet-activating protein S2
B, H
226Bordetella pertussisMutation(s): 0 
Gene Names: ptxBCYO81_20230ERS004697_00332ERS004704_00067ERS004709_00223ERS005128_00199ERS005179_00182ERS014547_00750NCTC10911_00247
UniProt
Find proteins for P04978 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251))
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UniProt GroupP04978
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Islet-activating protein S3
C, I
227Bordetella pertussisMutation(s): 0 
Gene Names: 
UniProt
Find proteins for P04979 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251))
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UniProt GroupP04979
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Islet-activating protein S4
D, E, J, K
152Bordetella pertussisMutation(s): 0 
Gene Names: ptxDCYO81_20235ERS005128_00198ERS005179_00181ERS014547_00749NCTC10911_00248
UniProt
Find proteins for P0A3R5 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251))
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UniProt GroupP0A3R5
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Pertussis toxin subunit 5
F, L
133Bordetella pertussisMutation(s): 0 
Gene Names: ptxEERS004697_00105ERS004704_00093ERS004709_00175ERS005128_00197ERS005179_00180ERS014547_00748ERS014550_01624ERS018341_00090
UniProt
Find proteins for P04981 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251))
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Go to UniProtKB:  P04981
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UniProt GroupP04981
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.241 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.464α = 90
b = 160.798β = 90
c = 194.829γ = 90
Software Package:
Software NamePurpose
autoBUSTERrefinement
XDSdata reduction
autoPROCdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2020-06-03 
  • Deposition Author(s): Bertrand, T.

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-03
    Type: Initial release
  • Version 1.1: 2020-09-02
    Changes: Database references, Refinement description
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description