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- EMDB-52739: L-PTC from Clostridium botulinum serotype B1, focused map of HA17... -

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Basic information

Entry
Database: EMDB / ID: EMD-52739
TitleL-PTC from Clostridium botulinum serotype B1, focused map of HA17-HA33 subcomplex (leg 1)
Map data
Sample
  • Complex: HA17-HA33 subcomplex from Clostridium botulinum serotype B1
    • Protein or peptide: Hemagglutinin component HA17
    • Protein or peptide: Hemagglutinin component HA33
    • Protein or peptide: Hemagglutinin component HA33
Keywordsprogenitor-toxin complex / botulinum neurotoxin / hemagglutinin / TOXIN
Function / homologyHemagglutinin component HA-17 / Clostridium botulinum HA-17 domain / Ricin-type beta-trefoil lectin domain-like / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Hemagglutinin component HA33 / Hemagglutinin component HA17
Function and homology information
Biological speciesClostridium botulinum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.62 Å
AuthorsKrc A / Persson Kosenina S / Masuyer G / Stenmark P
Funding support Sweden, Denmark, 2 items
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
DepositionFeb 5, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52739.png

Downloads & links

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Map

FileDownload / File: emd_52739.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 540 pix.
= 658.8 Å		1.22 Å/pix.
x 540 pix.
= 658.8 Å		1.22 Å/pix.
x 540 pix.
= 658.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.22 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.6361422 - 1.0383811
Average (Standard dev.)-0.0009360279 (±0.008381624)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 658.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_52739_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52739_half_map_2.map
Projections & Slices
AxesZYX

Projections

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HA17-HA33 subcomplex from Clostridium botulinum serotype B1

EntireName: HA17-HA33 subcomplex from Clostridium botulinum serotype B1
Components
  • Complex: HA17-HA33 subcomplex from Clostridium botulinum serotype B1
    • Protein or peptide: Hemagglutinin component HA17
    • Protein or peptide: Hemagglutinin component HA33
    • Protein or peptide: Hemagglutinin component HA33

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Supramolecule #1: HA17-HA33 subcomplex from Clostridium botulinum serotype B1

SupramoleculeName: HA17-HA33 subcomplex from Clostridium botulinum serotype B1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridium botulinum (bacteria)
Molecular weightTheoretical: 210 KDa

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Macromolecule #1: Hemagglutinin component HA17

MacromoleculeName: Hemagglutinin component HA17 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridium botulinum (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSAERTFLPN GNYNIKSIFS GSLYLSPVSG SLTFSNESSA NNQKWNVEYM AENRCFKISN VAEPNKYLSY DNFGFISLDS LSNRCYWFPI KIAVNTYIML SLNKVNELDY AWDIYDTNEN ILSQPLLLLP NFDIYNSNQM FKLEKI

UniProtKB: Hemagglutinin component HA17

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Macromolecule #2: Hemagglutinin component HA33

MacromoleculeName: Hemagglutinin component HA33 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Clostridium botulinum (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEHYSTIQNS LNDKIVTISC KANTDLFFYQ VPGNGNVSLF QQTRNYLERW RIIYDSNKAA YKIKSMNIYN TNLVLTWNAP THNISAQQDS NADNQYWLLL KDIGNNSFII ASYKNPNLVL YADTVARNLK LSTLNNSSYI KFIIEDYVIS DFKNFTCRIS PILAGGKVVQ ...String:
MEHYSTIQNS LNDKIVTISC KANTDLFFYQ VPGNGNVSLF QQTRNYLERW RIIYDSNKAA YKIKSMNIYN TNLVLTWNAP THNISAQQDS NADNQYWLLL KDIGNNSFII ASYKNPNLVL YADTVARNLK LSTLNNSSYI KFIIEDYVIS DFKNFTCRIS PILAGGKVVQ QVSMTNLAVN LYIWNNDLNQ KWTIIYNEEK AAYQFFNKIL SNGVLTWIFS DGNTVRVSSS AQNNDAQYWL INPVSDNYDR YTITNLRDKT KVLDLYGGQT ADGTTIQVFN SNGGDNQIWT MSNP

UniProtKB: Hemagglutinin component HA33

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Macromolecule #3: Hemagglutinin component HA33

MacromoleculeName: Hemagglutinin component HA33 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Clostridium botulinum (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEHYSTIQNS LNDKIVTISC KANTDLFFYQ VPGNGNVSLF QQTRNYLERW RIIYDSNKAA YKIKSMNIYN TNLVLTWNAP THNISAQQDS NADNQYWLLL KDIGNNSFII ASYKNPNLVL YADTVARNLK LSTLNNSSYI KFIIEDYVIS DFKNFTCRIS PILAGGKVVQ ...String:
MEHYSTIQNS LNDKIVTISC KANTDLFFYQ VPGNGNVSLF QQTRNYLERW RIIYDSNKAA YKIKSMNIYN TNLVLTWNAP THNISAQQDS NADNQYWLLL KDIGNNSFII ASYKNPNLVL YADTVARNLK LSTLNNSSYI KFIIEDYVIS DFKNFTCRIS PILAGGKVVQ QVSMTNLAVN LYIWNNDLNQ KWTIIYNEEK AAYQFFNKIL SNGVLTWIFS DGNTVRVSSS AQNNDAQYWL INPVSDNYDR YTITNLRDKT KVLDLYGGQT ADGTTIQVFN SNGGDNQIWT MSNP

UniProtKB: Hemagglutinin component HA33

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Details: Graphene oxide coating (0.2 mg/ml)
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 139594
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model

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