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- PDB-9qcm: Botulinum neurotoxin type B1, 14-subunit, Large Progenitor Toxin ... -

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Basic information

Entry
Database: PDB / ID: 9qcm
TitleBotulinum neurotoxin type B1, 14-subunit, Large Progenitor Toxin Complex (L-PTC)
Components
  • Botulinum neurotoxin type B
  • Botulinum neurotoxin type B1, nontoxic-nonhemagglutinin component, NTNH
  • Hemagglutinin component HA17
  • Hemagglutinin component HA33
  • Hemagglutinin component HA70
KeywordsTOXIN / progenitor-toxin complex / botulinum neurotoxin / hemagglutinin
Function / homology
Function and homology information


bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / lipid binding / host cell plasma membrane / proteolysis ...bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / lipid binding / host cell plasma membrane / proteolysis / extracellular region / zinc ion binding / membrane
Similarity search - Function
Hemagglutinin component HA-17 / Clostridium botulinum HA-17 domain / Nontoxic nonhaemagglutinin C-terminal / Nontoxic nonhaemagglutinin C-terminal / Botulinum neurotoxin, helical domain / Hemagglutinin component HA-70, C-terminal / Haemagglutinin 70 C-terminal domain / Clostridium enterotoxin / Clostridium enterotoxin / Ricin-type beta-trefoil lectin domain-like ...Hemagglutinin component HA-17 / Clostridium botulinum HA-17 domain / Nontoxic nonhaemagglutinin C-terminal / Nontoxic nonhaemagglutinin C-terminal / Botulinum neurotoxin, helical domain / Hemagglutinin component HA-70, C-terminal / Haemagglutinin 70 C-terminal domain / Clostridium enterotoxin / Clostridium enterotoxin / Ricin-type beta-trefoil lectin domain-like / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, N-terminal receptor binding / Ricin-type beta-trefoil / Kunitz inhibitor STI-like superfamily / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Botulinum neurotoxin type B / Botulinum neurotoxin type B1, nontoxic-nonhemagglutinin component, NTNH / Hemagglutinin component HA33 / Hemagglutinin component HA17 / Hemagglutinin component HA70
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsKrc, A. / Persson Kosenina, S. / Masuyer, G. / Stenmark, P.
Funding support Sweden, Denmark, 2items
OrganizationGrant numberCountry
Swedish Research Council2022-03681 Sweden
Novo Nordisk FoundationNNF20OC0064789 Denmark
CitationJournal: Sci Adv / Year: 2025
Title: Structure of the complete 14-subunit botulinum neurotoxin B complex reveals a unique anchoring through the narrow central pore of HA70.
Authors: Ajda Krč / Sara Persson Košenina / Maria B Nowakowska / Geoffrey Masuyer / Pål Stenmark /
Abstract: Botulinum neurotoxin serotype B1 (BoNT/B) is a highly potent neurotoxin and therapeutic agent. Here, we present the structure of the complete 14-subunit (780 kDa) progenitor toxin complex (L-PTC) and ...Botulinum neurotoxin serotype B1 (BoNT/B) is a highly potent neurotoxin and therapeutic agent. Here, we present the structure of the complete 14-subunit (780 kDa) progenitor toxin complex (L-PTC) and of five subcomplexes. The structures show how the toxin interacts with its associated components in their role to protect and deliver BoNT/B across epithelial barriers. Each subcomplex, including the M-PTC, M-PTC-HA70, NTNH-HA70, and HA70 trimer, provides detailed understanding of the assembly mechanism, in which the NTNH-nLoop adopts a unique fold that locks the M-PTC into a central pore formed by HA70. The HA subcomplex presents a tripod architecture with flexible legs that may adapt to the rugged cell surface. Mass photometry reveals the pH dependence of BoNT/B release from the complex which is unexpectedly influenced by the presence of HA70. This study provides the complete L-PTC structure, offering insights into its assemblage and supporting the development of countermeasures and therapeutic applications.
History
DepositionMar 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Botulinum neurotoxin type B
B: Botulinum neurotoxin type B1, nontoxic-nonhemagglutinin component, NTNH
C: Hemagglutinin component HA70
D: Hemagglutinin component HA70
E: Hemagglutinin component HA70
F: Hemagglutinin component HA17
G: Hemagglutinin component HA17
H: Hemagglutinin component HA17
I: Hemagglutinin component HA33
J: Hemagglutinin component HA33
K: Hemagglutinin component HA33
L: Hemagglutinin component HA33
M: Hemagglutinin component HA33
N: Hemagglutinin component HA33


Theoretical massNumber of molelcules
Total (without water)757,93414
Polymers757,93414
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

#1: Protein Botulinum neurotoxin type B / BoNT/B / Bontoxilysin-B


Mass: 152427.062 Da / Num. of mol.: 1 / Mutation: E232Q, H235Y
Source method: isolated from a genetically manipulated source
Details: 10x His tag on C-terminus, mutations E230Q, H233Y / Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botB, CLD_A0068 / Production host: Escherichia coli (E. coli) / References: UniProt: B1INP5
#2: Protein Botulinum neurotoxin type B1, nontoxic-nonhemagglutinin component, NTNH


Mass: 138876.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: ntnH, CLD_A0069 / Production host: Escherichia coli (E. coli) / References: UniProt: B1INP6, bontoxilysin
#3: Protein Hemagglutinin component HA70


Mass: 71249.336 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: ha70, CLD_A0073 / Production host: Escherichia coli (E. coli) / References: UniProt: B1INQ0
#4: Protein Hemagglutinin component HA17


Mass: 16919.018 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: ha17, CLD_A0072 / Production host: Escherichia coli (E. coli) / References: UniProt: B1INP9
#5: Protein
Hemagglutinin component HA33


Mass: 33687.562 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: ha33, CLD_A0071 / Production host: Escherichia coli (E. coli) / References: UniProt: B1INP8
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

Component
IDNameTypeEntity IDParent-IDSource
1Botulinum neurotoxin type B1 14-subunit Large Progenitor Toxin Complex (L-PTC)COMPLEXall0RECOMBINANT
2BoNT-NTNH complex or Minimal Progenitor Toxin Complex B1 (M-PTC)COMPLEX#1-#21RECOMBINANT
3HA70 trimerCOMPLEX#31RECOMBINANT
4HA17-HA33 subcomplex (legs)COMPLEX#4-#51RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.78 MDaNO
210.21 MDaYES
310.3 MDaNO
410.21 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Clostridium botulinum (bacteria)1491
22Clostridium botulinum (bacteria)1491
33Clostridium botulinum (bacteria)1491
44Clostridium botulinum (bacteria)1491
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Escherichia coli (E. coli)562
22Escherichia coli (E. coli)562
33Escherichia coli (E. coli)562
44Escherichia coli (E. coli)562
Buffer solutionpH: 5.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
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: 2400 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 139594 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model

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