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- EMDB-53015: Botulinum neurotoxin type B1, 14-subunit, Large Progenitor Toxin ... -

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Basic information

Entry
Database: EMDB / ID: EMD-53015
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)
    • Complex: BoNT-NTNH complex or Minimal Progenitor Toxin Complex B1 (M-PTC)
      • Protein or peptide: Botulinum neurotoxin type B
      • Protein or peptide: Botulinum neurotoxin type B1, nontoxic-nonhemagglutinin component, NTNH
    • Complex: HA70 trimer
      • Protein or peptide: Hemagglutinin component HA70
    • Complex: HA17-HA33 subcomplex (legs)
      • 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: 2.9 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_53015.png

Downloads & links

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Map

FileDownload / File: emd_53015.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
AxesX (Sec.)Y (Row.)Z (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: 4.0
Minimum - Maximum-33.058413999999999 - 74.185869999999994
Average (Standard dev.)-0.0030303295 (±1.0019809)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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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)
    • Complex: BoNT-NTNH complex or Minimal Progenitor Toxin Complex B1 (M-PTC)
      • Protein or peptide: Botulinum neurotoxin type B
      • Protein or peptide: Botulinum neurotoxin type B1, nontoxic-nonhemagglutinin component, NTNH
    • Complex: HA70 trimer
      • Protein or peptide: Hemagglutinin component HA70
    • Complex: HA17-HA33 subcomplex (legs)
      • 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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Supramolecule #2: BoNT-NTNH complex or Minimal Progenitor Toxin Complex B1 (M-PTC)

SupramoleculeName: BoNT-NTNH complex or Minimal Progenitor Toxin Complex B1 (M-PTC)
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Clostridium botulinum (bacteria)

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Supramolecule #3: HA70 trimer

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

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Supramolecule #4: HA17-HA33 subcomplex (legs)

SupramoleculeName: HA17-HA33 subcomplex (legs) / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4-#5
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 / Details: 10x His tag on C-terminus, mutations E230Q, H233Y / 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: Botulinum neurotoxin type B1, nontoxic-nonhemagglutinin component...

MacromoleculeName: Botulinum neurotoxin type B1, nontoxic-nonhemagglutinin component, NTNH
type: protein_or_peptide / ID: 2 / 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 #3: Hemagglutinin component HA70

MacromoleculeName: Hemagglutinin component HA70 / type: protein_or_peptide / ID: 3 / 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 #4: Hemagglutinin component HA17

MacromoleculeName: Hemagglutinin component HA17 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / 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 #5: Hemagglutinin component HA33

MacromoleculeName: Hemagglutinin component HA33 / type: protein_or_peptide / ID: 5 / Number of copies: 6 / 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: 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: 2.9 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
Output model

PDB-9qcm:
Botulinum neurotoxin type B1, 14-subunit, Large Progenitor Toxin Complex (L-PTC)

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