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- EMDB-53010: HA70-HA17-HA33 complex from Clostridium botulinum Serotype B1 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-53010
TitleHA70-HA17-HA33 complex from Clostridium botulinum Serotype B1
Map data
Sample
  • Complex: HA70-HA17-HA33 complex from botulinum neurotoxin serotype B1
    • Complex: HA70 trimer
      • Protein or peptide: Hemagglutinin component HA70
    • Complex: HA17-HA33 subcomplex
      • Protein or peptide: Hemagglutinin component HA17
      • Protein or peptide: Hemagglutinin component HA33
Keywordsprogenitor-toxin complex / botulinum neurotoxin / hemagglutinin / TOXIN
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Hemagglutinin component HA-17 / Clostridium botulinum HA-17 domain / Hemagglutinin component HA-70, C-terminal / Haemagglutinin 70 C-terminal domain / Clostridium enterotoxin / Clostridium enterotoxin / 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
Similarity search - Domain/homology
Hemagglutinin component HA33 / Hemagglutinin component HA17 / Hemagglutinin component HA70
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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
DepositionMar 4, 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_53010.png

Downloads & links

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Map

FileDownload / File: emd_53010.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.3 Å/pix.
x 320 pix.
= 416. Å		1.3 Å/pix.
x 320 pix.
= 416. Å		1.3 Å/pix.
x 320 pix.
= 416. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 11.199999999999999
Minimum - Maximum-38.147095 - 79.381709999999998
Average (Standard dev.)-0.00061381364 (±1.1643037)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 416.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : HA70-HA17-HA33 complex from botulinum neurotoxin serotype B1

EntireName: HA70-HA17-HA33 complex from botulinum neurotoxin serotype B1
Components
  • Complex: HA70-HA17-HA33 complex from botulinum neurotoxin serotype B1
    • Complex: HA70 trimer
      • Protein or peptide: Hemagglutinin component HA70
    • Complex: HA17-HA33 subcomplex
      • Protein or peptide: Hemagglutinin component HA17
      • Protein or peptide: Hemagglutinin component HA33

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Supramolecule #1: HA70-HA17-HA33 complex from botulinum neurotoxin serotype B1

SupramoleculeName: HA70-HA17-HA33 complex from botulinum neurotoxin 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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Supramolecule #2: HA70 trimer

SupramoleculeName: HA70 trimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Clostridium botulinum (bacteria)

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Supramolecule #3: HA17-HA33 subcomplex

SupramoleculeName: HA17-HA33 subcomplex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Clostridium botulinum (bacteria)

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Macromolecule #1: Hemagglutinin component HA70

MacromoleculeName: Hemagglutinin component HA70 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Clostridium botulinum (bacteria)
Molecular weightTheoretical: 71.249336 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNSSIKKIYN HIQEKVINYS DTIDLADGNY VVSRGDGWIL SRQNQILGGS VISNGSTGIV GDLRVNDNAI PYYYPTPSFN EEYIKNNIQ TVFANFTEAN QIPIGFEFSK TAPSNKNLYM YLQYTYIRYE IIKVLQHEII ERAVLYVPSL GYVKSIEFNP G EKINKDFY ...String:
MNSSIKKIYN HIQEKVINYS DTIDLADGNY VVSRGDGWIL SRQNQILGGS VISNGSTGIV GDLRVNDNAI PYYYPTPSFN EEYIKNNIQ TVFANFTEAN QIPIGFEFSK TAPSNKNLYM YLQYTYIRYE IIKVLQHEII ERAVLYVPSL GYVKSIEFNP G EKINKDFY FLTNDKCILN EQFLYKKILE TTKNIPTNNI FNSKVSSTQR VLPYSNGLYV INKGDGYIRT NDKDLIGTLL IE AGSSGSI IQPRLRNTTR PLFTTSNDAK FSQQYTEERL KDAFNVQLFN TSTSLFKFVE EAPSNKNICI KAYNTYEKYE LID YQNGSI VNKAEYYLPS LGYCEVTNAP SPESEVVKTQ VAEDGFIQNG PEEEIVVGVI DPSENIQEIN TAISDNYTYN IPGI VNNNP FYILFTVNTT GIYKINAQNN LPSLKIYEAI GSGNRNFQSG NLCDDDIKAI NYITGFDSPN AKSYLVVLLN KDKNY YIRV PQTSSNIENQ IKFKREEGDL RNLMNSSVNI IDNLNSTGAH YYTRQSPDVH DYISYEFTIP GNFNNKDTSN IRLYTS YNQ GIGTLFRVTE TIDGYNLINI QQNLNLLNST KSIRLLNGAI YILKVEVTEL NNYNIKLHID ITN

UniProtKB: Hemagglutinin component HA70

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Macromolecule #2: Hemagglutinin component HA17

MacromoleculeName: Hemagglutinin component HA17 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridium botulinum (bacteria)
Molecular weightTheoretical: 16.919018 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSAERTFLPN GNYNIKSIFS GSLYLSPVSG SLTFSNESSA NNQKWNVEYM AENRCFKISN VAEPNKYLSY DNFGFISLDS LSNRCYWFP IKIAVNTYIM LSLNKVNELD YAWDIYDTNE NILSQPLLLL PNFDIYNSNQ MFKLEKI

UniProtKB: Hemagglutinin component HA17

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Macromolecule #3: Hemagglutinin component HA33

MacromoleculeName: Hemagglutinin component HA33 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Clostridium botulinum (bacteria)
Molecular weightTheoretical: 33.687562 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEHYSTIQNS LNDKIVTISC KANTDLFFYQ VPGNGNVSLF QQTRNYLERW RIIYDSNKAA YKIKSMNIYN TNLVLTWNAP THNISAQQD SNADNQYWLL LKDIGNNSFI IASYKNPNLV LYADTVARNL KLSTLNNSSY IKFIIEDYVI SDFKNFTCRI S PILAGGKV ...String:
MEHYSTIQNS LNDKIVTISC KANTDLFFYQ VPGNGNVSLF QQTRNYLERW RIIYDSNKAA YKIKSMNIYN TNLVLTWNAP THNISAQQD SNADNQYWLL LKDIGNNSFI IASYKNPNLV LYADTVARNL KLSTLNNSSY IKFIIEDYVI SDFKNFTCRI S PILAGGKV VQQVSMTNLA VNLYIWNNDL NQKWTIIYNE EKAAYQFFNK ILSNGVLTWI FSDGNTVRVS SSAQNNDAQY WL INPVSDN YDRYTITNLR DKTKVLDLYG GQTADGTTIQ VFNSNGGDNQ IWTMSNP

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 R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
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 opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 130000
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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 524091
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
Output model

PDB-9qce:
HA70-HA17-HA33 complex from Clostridium botulinum Serotype B1

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