9MR7 | pdb_00009mr7

Genetiocally detoxified pertussis toxin in complex with hu1B7 Fab and hu11E6 Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.56 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural basis for neutralizing antibody binding to pertussis toxin.

Goldsmith, J.A.Nguyen, A.W.Wilen, R.E.Wijagkanalan, W.McLellan, J.S.Maynard, J.A.

(2025) Proc Natl Acad Sci U S A 122: e2419457122-e2419457122

  • DOI: https://doi.org/10.1073/pnas.2419457122
  • Primary Citation of Related Structures:  
    9MR7

  • PubMed Abstract: 

    Pertussis toxin (PT) is a key protective antigen in vaccine- and natural immunity-mediated protection from Bordetella pertussis infection. Despite its importance, no PT-neutralizing epitopes have been characterized structurally. To define neutralizing epitopes and identify key structural elements to preserve during PT antigen design, we determined a 3.6 Å cryoelectron microscopy structure of genetically detoxified PT (PTg) bound to hu11E6 and hu1B7, two potently neutralizing anti-PT antibodies with complementary mechanisms: disruption of toxin adhesion to cells and intracellular activities, respectively. Hu11E6 binds the paralogous S2 and S3 subunits of PTg via a conserved epitope but surprisingly did not span the previously identified sialic acid-binding site implicated in toxin adhesion. Hu11E6 specifically prevented PTg binding to sialylated N-glycans and a sialylated model receptor, as demonstrated by high-throughput glycan array analysis and ELISA, while a T cell activation assay showed that it blocks PTg mitogenic activities to define its neutralizing mechanism. Hu1B7 bound a quaternary epitope spanning the S1 and S5 subunits, although functional studies of hu1B7 variants suggested that S5 binding is not involved in its PT neutralization mechanism. These results structurally define neutralizing epitopes on PT, improving our molecular understanding of immune protection from B. pertussis and providing key information for the future development of PT immunogens.


  • Organizational Affiliation

    Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pertussis toxin subunit 1235Bordetella pertussisMutation(s): 0 
Gene Names: ptxABP3783
EC: 2.4.2
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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UniProt GroupP04977
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Pertussis toxin subunit 2199Bordetella pertussisMutation(s): 0 
Gene Names: ptxBBP3784
UniProt
Find proteins for P04978 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251))
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Go to UniProtKB:  P04978
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UniProt GroupP04978
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Pertussis toxin subunit 3199Bordetella pertussisMutation(s): 0 
Gene Names: ptxCBP3787
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
Pertussis toxin subunit 4
D, E
110Bordetella pertussisMutation(s): 0 
Gene Names: ptxDBP3785
UniProt
Find proteins for P0A3R5 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251))
Explore P0A3R5 
Go to UniProtKB:  P0A3R5
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UniProt GroupP0A3R5
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Pertussis toxin subunit 599Bordetella pertussisMutation(s): 0 
Gene Names: ptxEBP3786
UniProt
Find proteins for P04981 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251))
Explore P04981 
Go to UniProtKB:  P04981
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UniProt GroupP04981
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
hu1B7 Fab light chain213Mus musculusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
hu1B7 Fab heavy chain223Mus musculusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
hu11E6 Fab light chain
I, K
214Mus musculusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
hu11E6 Fab heavy chain
J, L
228Mus musculusMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.56 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI155453

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release