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- EMDB-53017: NTNH-HA70 complex from Clostridium botulinum Serotype B1 -

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Basic information

Entry
Database: EMDB / ID: EMD-53017
TitleNTNH-HA70 complex from Clostridium botulinum Serotype B1
Map data
Sample
  • Complex: NTNH-HA70 complex from botulinum neurotoxin serotype B1
    • Complex: HA70 trimer
      • Protein or peptide: Hemagglutinin component HA70
    • Complex: Non-toxic non-hemagglutinin protein B1
      • Protein or peptide: Botulinum neurotoxin type B1, nontoxic-nonhemagglutinin component, NTNH
Keywordsprogenitor-toxin complex / botulinum neurotoxin / hemagglutinin / TOXIN
Function / homology
Function and homology information


bontoxilysin / metalloendopeptidase activity / proteolysis / extracellular region / zinc ion binding
Similarity search - Function
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 / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain ...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 / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, N-terminal receptor binding / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Botulinum neurotoxin type B1, nontoxic-nonhemagglutinin component, NTNH / Hemagglutinin component HA70
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 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_53017.png

Downloads & links

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Map

FileDownload / File: emd_53017.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 400 pix.
= 331.2 Å		0.83 Å/pix.
x 400 pix.
= 331.2 Å		0.83 Å/pix.
x 400 pix.
= 331.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.44
Minimum - Maximum-30.364007999999998 - 52.123733999999999
Average (Standard dev.)-0.00056961656 (±1.1808265)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 331.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : NTNH-HA70 complex from botulinum neurotoxin serotype B1

EntireName: NTNH-HA70 complex from botulinum neurotoxin serotype B1
Components
  • Complex: NTNH-HA70 complex from botulinum neurotoxin serotype B1
    • Complex: HA70 trimer
      • Protein or peptide: Hemagglutinin component HA70
    • Complex: Non-toxic non-hemagglutinin protein B1
      • Protein or peptide: Botulinum neurotoxin type B1, nontoxic-nonhemagglutinin component, NTNH

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

SupramoleculeName: NTNH-HA70 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 #3: HA70 trimer

SupramoleculeName: HA70 trimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Clostridium botulinum (bacteria)

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Supramolecule #2: Non-toxic non-hemagglutinin protein B1

SupramoleculeName: Non-toxic non-hemagglutinin protein B1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Clostridium botulinum (bacteria)

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Macromolecule #1: Botulinum neurotoxin type B1, nontoxic-nonhemagglutinin component...

MacromoleculeName: Botulinum neurotoxin type B1, nontoxic-nonhemagglutinin component, NTNH
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: bontoxilysin
Source (natural)Organism: Clostridium botulinum (bacteria)
Molecular weightTheoretical: 138.876797 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNINDNLSIN SPVDNKNVVV VRARKTDTVF KAFKVAPNIW VAPERYYGES LSIDEEYKVD GGIYDSNFLS QDSEKDKFLQ AIITLLKRI NSTNAGEKLL SLISTAIPFP YGYIGGGYYA PNMITFGSAP KSNKKLNSLI SSTIPFPYAG YRETNYLSSE D NKSFYASN ...String:
MNINDNLSIN SPVDNKNVVV VRARKTDTVF KAFKVAPNIW VAPERYYGES LSIDEEYKVD GGIYDSNFLS QDSEKDKFLQ AIITLLKRI NSTNAGEKLL SLISTAIPFP YGYIGGGYYA PNMITFGSAP KSNKKLNSLI SSTIPFPYAG YRETNYLSSE D NKSFYASN IVIFGPGANI VENNTVFYKK EDAENGMGTM TEIWFQPFLT YKYDEFYIDP AIELIKCLIK SLYFLYGIKP SD DLVIPYR LRSELENIEY SQLNIVDLLV SGGIDPKFIN TDPYWFTDNY FSNAKKVFED HRNIYETQIE GNNAIGNDIK LRL KQKFRI NINDIWELNL NYFSKEFSIM MPDRFNNALK HFYRKQYYKI DYPENYSING FVNGQINVQL SLSDRNQDII NKPE EIINL LNGNNVSLMR SNIYGDGLKS TVDDFYSNYK IPYNRAYEYH FNNSNDSSLD NVNIGVIDNI PEIIDVNPYK ENCDK FSPV QKITSTREIN TNIPWPINYL QAQNTNNEKF SLSSDFVEVV SSKDKSLVYS FLSNVMFYLD SIKDNSPIDT DKKYYL WLR EIFRNYSFDI TATQEINTDC GINKVVTWFG KALNILNTSD SFVEEFQNLG PISLINKKEN LSMPIIEIYG IPNDMLG LP LNDLNEKLFN IYLKNILYFK KVYFNFLDQW WTEYYSQYFD LICMAKQSIL AQEKLIKQII QNKLQDLFKA DISMDKLN L MNLATEKTFI DLSNESQIAI NNINDFLNKS AICVFDTNIY PKFISFMEQC INSVNSNVTA FIQKCTNITE DEKLQLIKL NTFMNIDFEF FDIQSIKDLI TSETDLIKEE KESDYNLFLF TLQEDNNKVI EDISGKNTLV KYSDSISLVY GVNGDALYLK EPDESVSFS NKAFENGLTN SFSICFWLRN LGEDIITSKL IENKADNCGW EIYFENNGLV FSIVDCNGNE ENIYLSDVIS K NWYYISIS IDRLRNQLLI FINDKLIANQ SIEQILNIYS SNTISLVNEN NPIYIEGLSI LNRSITSEEV VNNYFSYLNN SY IRDISGE RLEYNKTYEL YNYVFPENSL YEVTENNNIY LSIKDTNNLN IQGAKFKLIN IDANKQYVQK WDEGVVCLLG DEE KYVDIS SENNRIQLVN SKDTAKRIIF NNDIFMPNCL TFAYNNKYLS LSLRDRNYNW MICNNNDNIP KAAHLWALKG I

UniProtKB: Botulinum neurotoxin type B1, nontoxic-nonhemagglutinin component, NTNH

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Macromolecule #2: Hemagglutinin component HA70

MacromoleculeName: Hemagglutinin component HA70 / type: protein_or_peptide / ID: 2 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 5.5
GridModel: Quantifoil Active R2/1 / Material: COPPER / Mesh: 300 / 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: 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: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 355719
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-9qco:
NTNH-HA70 complex from Clostridium botulinum Serotype B1

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