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- EMDB-52743: L-PTC from Clostridium botulinum serotype B1, focused map of BoNT... -

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Basic information

Entry
Database: EMDB / ID: EMD-52743
TitleL-PTC from Clostridium botulinum serotype B1, focused map of BoNT-NTNH subcomplex
Map data
Sample
  • Complex: BoNT-NTNH subcomplex from Clostridium botulinum serotype B1
    • Protein or peptide: Botulinum neurotoxin B1
    • Protein or peptide: Non-toxic non-hemagglutinin protein B1
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
Nontoxic nonhaemagglutinin C-terminal / Nontoxic nonhaemagglutinin C-terminal / Botulinum neurotoxin, helical domain / 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 ...Nontoxic nonhaemagglutinin C-terminal / Nontoxic nonhaemagglutinin C-terminal / Botulinum neurotoxin, helical domain / 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 / Kunitz inhibitor STI-like superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Botulinum neurotoxin type B / Non-toxic non-hemagglutinin component
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 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_52743.png

Downloads & links

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Map

FileDownload / File: emd_52743.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: 0.158
Minimum - Maximum-0.6659214 - 1.378736
Average (Standard dev.)-0.0006578976 (±0.02124141)
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_52743_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_52743_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BoNT-NTNH subcomplex from Clostridium botulinum serotype B1

EntireName: BoNT-NTNH subcomplex from Clostridium botulinum serotype B1
Components
  • Complex: BoNT-NTNH subcomplex from Clostridium botulinum serotype B1
    • Protein or peptide: Botulinum neurotoxin B1
    • Protein or peptide: Non-toxic non-hemagglutinin protein B1

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Supramolecule #1: BoNT-NTNH subcomplex from Clostridium botulinum serotype B1

SupramoleculeName: BoNT-NTNH 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: 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 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: Non-toxic non-hemagglutinin component

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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: 120 sec. / Details: Graphene oxide coating
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: 2.83 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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