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- PDB-9e3k: Cryo EM structure of pertussis toxin in complex with neutralizing... -

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Basic information

Entry
Database: PDB / ID: 9e3k
TitleCryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-199
Components
  • (Pertussis toxin subunit ...) x 4
  • Islet-activating protein S2
  • PERT-199 HC
  • PERT-199 LC
KeywordsTOXIN/Immune System / PTx / mAb / Whooping / TOXIN / TOXIN-Immune System complex
Function / homology
Function and homology information


NAD+ poly-ADP-ribosyltransferase 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 B, subunit 2/3, C-terminal / Pertussis toxin, subunit 2 and 3, C-terminal domain / Bordetella pertussis toxin A / Pertussis toxin, subunit 1 / 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 B, subunit 2/3, C-terminal / Pertussis toxin, subunit 2 and 3, C-terminal domain / Bordetella pertussis toxin A / Pertussis toxin, subunit 1 / 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
Islet-activating protein S2 / Pertussis toxin subunit 3 / Pertussis toxin subunit 5 / Pertussis toxin subunit 4 / Pertussis toxin subunit 1
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBinshtein, E. / Crowe, J.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-199
Authors: Binshtein, E. / Crowe, J.E.
History
DepositionOct 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pertussis toxin subunit 1
B: Islet-activating protein S2
C: Pertussis toxin subunit 3
D: Pertussis toxin subunit 4
E: Pertussis toxin subunit 4
F: Pertussis toxin subunit 5
H: PERT-199 HC
K: PERT-199 LC
L: PERT-199 LC
J: PERT-199 HC


Theoretical massNumber of molelcules
Total (without water)178,78110
Polymers178,78110
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Pertussis toxin subunit ... , 4 types, 5 molecules ACDEF

#1: Protein Pertussis toxin subunit 1


Mass: 30005.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: ptxA / Production host: Bordetella pertussis (bacteria) / References: UniProt: T1SR96
#3: Protein Pertussis toxin subunit 3 / PTX S3 / Islet-activating protein S3 / IAP S3


Mass: 25012.820 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: 16566.744 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: 14513.755 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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Protein , 1 types, 1 molecules B

#2: Protein Islet-activating protein S2


Mass: 24856.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: ptxB, NCTC10911_00247 / Production host: Bordetella pertussis (bacteria) / References: UniProt: A0A0E8DFW5

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Antibody , 2 types, 4 molecules HJKL

#6: Antibody PERT-199 HC


Mass: 14149.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#7: Antibody PERT-199 LC


Mass: 11479.811 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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: pertussis toxin in complex with neutralizing Fab PERT-199
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Bordetella pertussis (bacteria)
Buffer solutionpH: 8
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 magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 16142
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
2EPUimage acquisition
7Cootmodel fitting
9PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 508875 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410248
ELECTRON MICROSCOPYf_angle_d0.62713915
ELECTRON MICROSCOPYf_dihedral_angle_d4.7131465
ELECTRON MICROSCOPYf_chiral_restr0.0431534
ELECTRON MICROSCOPYf_plane_restr0.0061795

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