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- EMDB-52763: Botulinum neurotoxin type B1 14-subunit Large Progenitor Toxin Co... -

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Basic information

Entry
Database: EMDB / ID: EMD-52763
TitleBotulinum neurotoxin type B1 14-subunit Large Progenitor Toxin Complex (L-PTC)
Map data
Sample
  • Complex: Botulinum neurotoxin type B1 14-subunit Large Progenitor Toxin Complex (L-PTC)
    • Protein or peptide: Botulinum neurotoxin B1
    • Protein or peptide: Non-toxic non-hemagglutinin protein B1
    • Protein or peptide: Hemagglutinin component HA70
    • 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


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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 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 6, 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_52763.png

Downloads & links

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Map

FileDownload / File: emd_52763.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.
= 659.988 Å		1.22 Å/pix.
x 540 pix.
= 659.988 Å		1.22 Å/pix.
x 540 pix.
= 659.988 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2222 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0583
Minimum - Maximum-0.52816767 - 1.1944833
Average (Standard dev.)-0.00065580354 (±0.015774764)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 659.98804 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_52763_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_52763_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Botulinum neurotoxin type B1 14-subunit Large Progenitor Toxin Co...

EntireName: Botulinum neurotoxin type B1 14-subunit Large Progenitor Toxin Complex (L-PTC)
Components
  • Complex: Botulinum neurotoxin type B1 14-subunit Large Progenitor Toxin Complex (L-PTC)
    • Protein or peptide: Botulinum neurotoxin B1
    • Protein or peptide: Non-toxic non-hemagglutinin protein B1
    • Protein or peptide: Hemagglutinin component HA70
    • Protein or peptide: Hemagglutinin component HA17
    • Protein or peptide: Hemagglutinin component HA33

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Supramolecule #1: Botulinum neurotoxin type B1 14-subunit Large Progenitor Toxin Co...

SupramoleculeName: Botulinum neurotoxin type B1 14-subunit Large Progenitor Toxin Complex (L-PTC)
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: Botulinum neurotoxin B1

MacromoleculeName: Botulinum neurotoxin B1 / type: protein_or_peptide / ID: 1 / Details: 10x His tag on C-terminus, mutations E230Q, H233Y / Enantiomer: LEVO
Source (natural)Organism: Clostridium botulinum (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGPVTINNFN YNDPIDNNNI IMMEPPFARG TGRYYKAFKI TDRIWIIPER YTFGYKPEDF NKSSGIFNRD VCEYYDPDYL NTNDKKNIFL QTMIKLFNRI KSKPLGEKLL EMIINGIPYL GDRRVPLEEF NTNIASVTVN KLISNPGEVE RKKGIFANLI IFGPGPVLNE ...String:
MGPVTINNFN YNDPIDNNNI IMMEPPFARG TGRYYKAFKI TDRIWIIPER YTFGYKPEDF NKSSGIFNRD VCEYYDPDYL NTNDKKNIFL QTMIKLFNRI KSKPLGEKLL EMIINGIPYL GDRRVPLEEF NTNIASVTVN KLISNPGEVE RKKGIFANLI IFGPGPVLNE NETIDIGIQN HFASREGFGG IMQMKFCPEY VSVFNNVQEN KGASIFNRRG YFSDPALILM HQLIYVLHGL YGIKVDDLPI VPNEKKFFMQ STDAIQAEEL YTFGGQDPSI ITPSTDKSIY DKVLQNFRGI VDRLNKVLVC ISDPNININI YKNKFKDKYK FVEDSEGKYS IDVESFDKLY KSLMFGFTET NIAENYKIKT RASYFSDSLP PVKIKNLLDN EIYTIEEGFN ISDKDMEKEY RGQNKAINKQ AYEEISKEHL AVYKIQMCKS VKAPGICIDV DNEDLFFIAD KNSFSDDLSK NERIEYNTQS NYIENDFPIN ELILDTDLIS KIELPSENTE SLTDFNVDVP VYEKQPAIKK IFTDENTIFQ YLYSQTFPLD IRDISLTSSF DDALLFSNKV YSFFSMDYIK TANKVVEAGL FAGWVKQIVN DFVIEANKSN TMDKIADISL IVPYIGLALN VGNETAKGNF ENAFEIAGAS ILLEFIPELL IPVVGAFLLE SYIDNKNKII KTIDNALTKR NEKWSDMYGL IVAQWLSTVN TQFYTIKEGM YKALNYQAQA LEEIIKYRYN IYSEKEKSNI NIDFNDINSK LNEGINQAID NINNFINGCS VSYLMKKMIP LAVEKLLDFD NTLKKNLLNY IDENKLYLIG SAEYEKSKVN KYLKTIMPFD LSIYTNDTIL IEMFNKYNSE ILNNIILNLR YKDNNLIDLS GYGAKVEVYD GVELNDKNQF KLTSSANSKI RVTQNQNIIF NSVFLDFSVS FWIRIPKYKN DGIQNYIHNE YTIINCMKNN SGWKISIRGN RIIWTLIDIN GKTKSVFFEY NIREDISEYI NRWFFVTITN NLNNAKIYIN GKLESNTDIK DIREVIANGE IIFKLDGDID RTQFIWMKYF SIFNTELSQS NIEERYKIQS YSEYLKDFWG NPLMYNKEYY MFNAGNKNSY IKLKKDSPVG EILTRSKYNQ NSKYINYRDL YIGEKFIIRR KSNSQSINDD IVRKEDYIYL DFFNLNQEWR VYTYKYFKKE EEKLFLAPIS DSDEFYNTIQ IKEYDEQPTY SCQLLFKKDE ESTDEIGLIG IHRFYESGIV FEEYKDYFCI SKWYLKEVKR KPYNLKLGCN WQFIPKDEGW TEHHHHHHHH HH

UniProtKB: Botulinum neurotoxin type B

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

MacromoleculeName: Non-toxic non-hemagglutinin protein B1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Clostridium botulinum (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNINDNLSIN SPVDNKNVVV VRARKTDTVF KAFKVAPNIW VAPERYYGES LSIDEEYKVD GGIYDSNFLS QDSEKDKFLQ AIITLLKRIN STNAGEKLLS LISTAIPFPY GYIGGGYYAP NMITFGSAPK SNKKLNSLIS STIPFPYAGY RETNYLSSED NKSFYASNIV ...String:
MNINDNLSIN SPVDNKNVVV VRARKTDTVF KAFKVAPNIW VAPERYYGES LSIDEEYKVD GGIYDSNFLS QDSEKDKFLQ AIITLLKRIN STNAGEKLLS LISTAIPFPY GYIGGGYYAP NMITFGSAPK SNKKLNSLIS STIPFPYAGY RETNYLSSED NKSFYASNIV IFGPGANIVE NNTVFYKKED AENGMGTMTE IWFQPFLTYK YDEFYIDPAI ELIKCLIKSL YFLYGIKPSD DLVIPYRLRS ELENIEYSQL NIVDLLVSGG IDPKFINTDP YWFTDNYFSN AKKVFEDHRN IYETQIEGNN AIGNDIKLRL KQKFRININD IWELNLNYFS KEFSIMMPDR FNNALKHFYR KQYYKIDYPE NYSINGFVNG QINVQLSLSD RNQDIINKPE EIINLLNGNN VSLMRSNIYG DGLKSTVDDF YSNYKIPYNR AYEYHFNNSN DSSLDNVNIG VIDNIPEIID VNPYKENCDK FSPVQKITST REINTNIPWP INYLQAQNTN NEKFSLSSDF VEVVSSKDKS LVYSFLSNVM FYLDSIKDNS PIDTDKKYYL WLREIFRNYS FDITATQEIN TDCGINKVVT WFGKALNILN TSDSFVEEFQ NLGPISLINK KENLSMPIIE IYGIPNDMLG LPLNDLNEKL FNIYLKNILY FKKVYFNFLD QWWTEYYSQY FDLICMAKQS ILAQEKLIKQ IIQNKLQDLF KADISMDKLN LMNLATEKTF IDLSNESQIA INNINDFLNK SAICVFDTNI YPKFISFMEQ CINSVNSNVT AFIQKCTNIT EDEKLQLIKL NTFMNIDFEF FDIQSIKDLI TSETDLIKEE KESDYNLFLF TLQEDNNKVI EDISGKNTLV KYSDSISLVY GVNGDALYLK EPDESVSFSN KAFENGLTNS FSICFWLRNL GEDIITSKLI ENKADNCGWE IYFENNGLVF SIVDCNGNEE NIYLSDVISK NWYYISISID RLRNQLLIFI NDKLIANQSI EQILNIYSSN TISLVNENNP IYIEGLSILN RSITSEEVVN NYFSYLNNSY IRDISGERLE YNKTYELYNY VFPENSLYEV TENNNIYLSI KDTNNLNIQG AKFKLINIDA NKQYVQKWDE GVVCLLGDEE KYVDISSENN RIQLVNSKDT AKRIIFNNDI FMPNCLTFAY NNKYLSLSLR DRNYNWMICN NNDNIPKAAH LWALKGI

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

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Macromolecule #3: Hemagglutinin component HA70

MacromoleculeName: Hemagglutinin component HA70 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Clostridium botulinum (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNSSIKKIYN HIQEKVINYS DTIDLADGNY VVSRGDGWIL SRQNQILGGS VISNGSTGIV GDLRVNDNAI PYYYPTPSFN EEYIKNNIQT VFANFTEANQ IPIGFEFSKT APSNKNLYMY LQYTYIRYEI IKVLQHEIIE RAVLYVPSLG YVKSIEFNPG EKINKDFYFL ...String:
MNSSIKKIYN HIQEKVINYS DTIDLADGNY VVSRGDGWIL SRQNQILGGS VISNGSTGIV GDLRVNDNAI PYYYPTPSFN EEYIKNNIQT VFANFTEANQ IPIGFEFSKT APSNKNLYMY LQYTYIRYEI IKVLQHEIIE RAVLYVPSLG YVKSIEFNPG EKINKDFYFL TNDKCILNEQ FLYKKILETT KNIPTNNIFN SKVSSTQRVL PYSNGLYVIN KGDGYIRTND KDLIGTLLIE AGSSGSIIQP RLRNTTRPLF TTSNDAKFSQ QYTEERLKDA FNVQLFNTST SLFKFVEEAP SNKNICIKAY NTYEKYELID YQNGSIVNKA EYYLPSLGYC EVTNAPSPES EVVKTQVAED GFIQNGPEEE IVVGVIDPSE NIQEINTAIS DNYTYNIPGI VNNNPFYILF TVNTTGIYKI NAQNNLPSLK IYEAIGSGNR NFQSGNLCDD DIKAINYITG FDSPNAKSYL VVLLNKDKNY YIRVPQTSSN IENQIKFKRE EGDLRNLMNS SVNIIDNLNS TGAHYYTRQS PDVHDYISYE FTIPGNFNNK DTSNIRLYTS YNQGIGTLFR VTETIDGYNL INIQQNLNLL NSTKSIRLLN GAIYILKVEV TELNNYNIKL HIDITN

UniProtKB: Hemagglutinin component HA70

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Macromolecule #4: Hemagglutinin component HA17

MacromoleculeName: Hemagglutinin component HA17 / type: protein_or_peptide / ID: 4 / 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 #5: Hemagglutinin component HA33

MacromoleculeName: Hemagglutinin component HA33 / type: protein_or_peptide / ID: 5 / 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: 5.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 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 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: 2.91 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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