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- PDB-9mr7: Genetiocally detoxified pertussis toxin in complex with hu1B7 Fab... -

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Basic information

Entry
Database: PDB / ID: 9mr7
TitleGenetiocally detoxified pertussis toxin in complex with hu1B7 Fab and hu11E6 Fab
Components
  • (Pertussis toxin subunit ...) x 5
  • hu11E6 Fab heavy chain
  • hu11E6 Fab light chain
  • hu1B7 Fab heavy chain
  • hu1B7 Fab light chain
KeywordsTOXIN / Pertussis / Antibody
Function / homology
Function and homology information


NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / toxin activity / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Bordetella pertussis toxin B / Pertussis toxin, subunit S4 / Pertussis toxin, subunit S5 / Pertussis toxin S4 subunit / Pertussis toxin S5 subunit / Bordetella pertussis toxin A / Pertussis toxin, subunit 1 / Bordetella pertussis toxin B, subunit 2/3, C-terminal / Pertussis toxin, subunit 2 and 3, C-terminal domain / Aerolysin/Pertussis toxin domain ...Bordetella pertussis toxin B / Pertussis toxin, subunit S4 / Pertussis toxin, subunit S5 / Pertussis toxin S4 subunit / Pertussis toxin S5 subunit / Bordetella pertussis toxin A / Pertussis toxin, subunit 1 / Bordetella pertussis toxin B, subunit 2/3, C-terminal / Pertussis toxin, subunit 2 and 3, C-terminal domain / Aerolysin/Pertussis toxin domain / Aerolysin/Pertussis toxin (APT), N-terminal domain superfamily / Aerolysin/Pertussis toxin (APT) domain / Enterotoxin / C-type lectin fold
Similarity search - Domain/homology
Pertussis toxin subunit 1 / Pertussis toxin subunit 2 / Pertussis toxin subunit 3 / Pertussis toxin subunit 5 / Pertussis toxin subunit 4
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsGoldsmith, J.A. / McLellan, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI155453 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structural basis for neutralizing antibody binding to pertussis toxin.
Authors: Jory A Goldsmith / Annalee W Nguyen / Rebecca E Wilen / Wassana Wijagkanalan / Jason S McLellan / Jennifer A Maynard /
Abstract: Pertussis toxin (PT) is a key protective antigen in vaccine- and natural immunity-mediated protection from infection. Despite its importance, no PT-neutralizing epitopes have been characterized ...Pertussis toxin (PT) is a key protective antigen in vaccine- and natural immunity-mediated protection from 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 and providing key information for the future development of PT immunogens.
History
DepositionJan 7, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pertussis toxin subunit 1
B: Pertussis toxin subunit 2
C: Pertussis toxin subunit 3
D: Pertussis toxin subunit 4
E: Pertussis toxin subunit 4
F: Pertussis toxin subunit 5
G: hu1B7 Fab light chain
H: hu1B7 Fab heavy chain
I: hu11E6 Fab light chain
J: hu11E6 Fab heavy chain
K: hu11E6 Fab light chain
L: hu11E6 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)248,36612
Polymers248,36612
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Pertussis toxin subunit ... , 5 types, 6 molecules ABCDEF

#1: Protein Pertussis toxin subunit 1 / PTX S1 / Islet-activating protein S1 / IAP S1 / NAD-dependent ADP-ribosyltransferase


Mass: 26148.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: ptxA, BP3783 / Production host: Bordetella pertussis (bacteria)
References: UniProt: P04977, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Protein Pertussis toxin subunit 2 / PTX S2 / Islet-activating protein S2 / IAP S2


Mass: 21913.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: ptxB, BP3784 / Production host: Bordetella pertussis (bacteria) / References: UniProt: P04978
#3: Protein Pertussis toxin subunit 3 / PTX S3 / Islet-activating protein S3 / IAP S3


Mass: 21889.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: ptxC, BP3787 / Production host: Bordetella pertussis (bacteria) / References: UniProt: P04979
#4: Protein Pertussis toxin subunit 4 / PTX S4 / Islet-activating protein S4 / IAP S4


Mass: 12072.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: ptxD, BP3785 / Production host: Bordetella pertussis (bacteria) / References: UniProt: P0A3R5
#5: Protein Pertussis toxin subunit 5 / PTX S5 / Islet-activating protein S5 / IAP S5


Mass: 10951.524 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: ptxE, BP3786 / Production host: Bordetella pertussis (bacteria) / References: UniProt: P04981

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Antibody , 4 types, 6 molecules GHIKJL

#6: Antibody hu1B7 Fab light chain


Mass: 23137.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#7: Antibody hu1B7 Fab heavy chain


Mass: 23868.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#8: Antibody hu11E6 Fab light chain


Mass: 23421.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#9: Antibody hu11E6 Fab heavy chain


Mass: 24733.768 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ternary complex of integrin alphaM/beta2 ectodomain with adenylate cyclase toxin RTX domain and M1F5 Fab
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 316937 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 61.87 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00312771
ELECTRON MICROSCOPYf_angle_d0.663417343
ELECTRON MICROSCOPYf_chiral_restr0.04921896
ELECTRON MICROSCOPYf_plane_restr0.00772220
ELECTRON MICROSCOPYf_dihedral_angle_d12.2664602

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