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- EMDB-53005: BoNT-NTNH complex from Clostridium botulinum Serotype B1 -

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Basic information

Entry
Database: EMDB / ID: EMD-53005
TitleBoNT-NTNH complex from Clostridium botulinum Serotype B1
Map data
Sample
  • Complex: M-PTC from botulinum neurotoxin serotype B1
    • Complex: minimal progenitor toxin complex from serotype B1
      • Complex: Botulinum neurotoxin serotype B1
        • Protein or peptide: Botulinum neurotoxin type B
      • Complex: Non-toxic non-hemagglutinin protein B1
        • Protein or peptide: Non-toxic non-hemagglutinin component
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: 2.67 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_53005.png

Downloads & links

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Map

FileDownload / File: emd_53005.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 350 pix.
= 301. Å		0.86 Å/pix.
x 350 pix.
= 301. Å		0.86 Å/pix.
x 350 pix.
= 301. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.151
Minimum - Maximum-0.26786923 - 0.90633047
Average (Standard dev.)0.0025472296 (±0.025499886)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 301.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53005_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53005_half_map_2.map
Projections & Slices
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Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : M-PTC from botulinum neurotoxin serotype B1

EntireName: M-PTC from botulinum neurotoxin serotype B1
Components
  • Complex: M-PTC from botulinum neurotoxin serotype B1
    • Complex: minimal progenitor toxin complex from serotype B1
      • Complex: Botulinum neurotoxin serotype B1
        • Protein or peptide: Botulinum neurotoxin type B
      • Complex: Non-toxic non-hemagglutinin protein B1
        • Protein or peptide: Non-toxic non-hemagglutinin component

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Supramolecule #1: M-PTC from botulinum neurotoxin serotype B1

SupramoleculeName: M-PTC 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: minimal progenitor toxin complex from serotype B1

SupramoleculeName: minimal progenitor toxin complex from serotype B1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Clostridium botulinum (bacteria)

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Supramolecule #3: Botulinum neurotoxin serotype B1

SupramoleculeName: Botulinum neurotoxin serotype B1 / type: complex / ID: 3 / Parent: 2 / Macromolecule list: #1
Source (natural)Organism: Clostridium botulinum (bacteria)

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Supramolecule #4: Non-toxic non-hemagglutinin protein B1

SupramoleculeName: Non-toxic non-hemagglutinin protein B1 / type: complex / ID: 4 / Parent: 2 / Macromolecule list: #2
Source (natural)Organism: Clostridium botulinum (bacteria)

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Macromolecule #1: Botulinum neurotoxin type B

MacromoleculeName: Botulinum neurotoxin type B / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridium botulinum (bacteria)
Molecular weightTheoretical: 152.427062 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGPVTINNFN YNDPIDNNNI IMMEPPFARG TGRYYKAFKI TDRIWIIPER YTFGYKPEDF NKSSGIFNRD VCEYYDPDYL NTNDKKNIF LQTMIKLFNR IKSKPLGEKL LEMIINGIPY LGDRRVPLEE FNTNIASVTV NKLISNPGEV ERKKGIFANL I IFGPGPVL ...String:
MGPVTINNFN YNDPIDNNNI IMMEPPFARG TGRYYKAFKI TDRIWIIPER YTFGYKPEDF NKSSGIFNRD VCEYYDPDYL NTNDKKNIF LQTMIKLFNR IKSKPLGEKL LEMIINGIPY LGDRRVPLEE FNTNIASVTV NKLISNPGEV ERKKGIFANL I IFGPGPVL NENETIDIGI QNHFASREGF GGIMQMKFCP EYVSVFNNVQ ENKGASIFNR RGYFSDPALI LMHQLIYVLH GL YGIKVDD LPIVPNEKKF FMQSTDAIQA EELYTFGGQD PSIITPSTDK SIYDKVLQNF RGIVDRLNKV LVCISDPNIN INI YKNKFK DKYKFVEDSE GKYSIDVESF DKLYKSLMFG FTETNIAENY KIKTRASYFS DSLPPVKIKN LLDNEIYTIE EGFN ISDKD MEKEYRGQNK AINKQAYEEI SKEHLAVYKI QMCKSVKAPG ICIDVDNEDL FFIADKNSFS DDLSKNERIE YNTQS NYIE NDFPINELIL DTDLISKIEL PSENTESLTD FNVDVPVYEK QPAIKKIFTD ENTIFQYLYS QTFPLDIRDI SLTSSF DDA LLFSNKVYSF FSMDYIKTAN KVVEAGLFAG WVKQIVNDFV IEANKSNTMD KIADISLIVP YIGLALNVGN ETAKGNF EN AFEIAGASIL LEFIPELLIP VVGAFLLESY IDNKNKIIKT IDNALTKRNE KWSDMYGLIV AQWLSTVNTQ FYTIKEGM Y KALNYQAQAL EEIIKYRYNI YSEKEKSNIN IDFNDINSKL NEGINQAIDN INNFINGCSV SYLMKKMIPL AVEKLLDFD NTLKKNLLNY IDENKLYLIG SAEYEKSKVN KYLKTIMPFD LSIYTNDTIL IEMFNKYNSE ILNNIILNLR YKDNNLIDLS GYGAKVEVY DGVELNDKNQ FKLTSSANSK IRVTQNQNII FNSVFLDFSV SFWIRIPKYK NDGIQNYIHN EYTIINCMKN N SGWKISIR GNRIIWTLID INGKTKSVFF EYNIREDISE YINRWFFVTI TNNLNNAKIY INGKLESNTD IKDIREVIAN GE IIFKLDG DIDRTQFIWM KYFSIFNTEL SQSNIEERYK IQSYSEYLKD FWGNPLMYNK EYYMFNAGNK NSYIKLKKDS PVG EILTRS KYNQNSKYIN YRDLYIGEKF IIRRKSNSQS INDDIVRKED YIYLDFFNLN QEWRVYTYKY FKKEEEKLFL APIS DSDEF YNTIQIKEYD EQPTYSCQLL FKKDEESTDE IGLIGIHRFY ESGIVFEEYK DYFCISKWYL KEVKRKPYNL KLGCN WQFI PKDEGWTEHH HHHHHHHH

UniProtKB: Botulinum neurotoxin type B

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Macromolecule #2: Non-toxic non-hemagglutinin component

MacromoleculeName: Non-toxic non-hemagglutinin component / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
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: 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: 5.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
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: 2.6 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 correctionDetails: CTF amplitude correction was performed following 3D reconstruction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 280361
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-9qc7:
BoNT-NTNH complex from Clostridium botulinum Serotype B1

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