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- PDB-9ea9: Crystal structure of BoNT/A-NTNH-HA70 -VHH_F12-VHH_H7-Fab_NTNH complex -

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Basic information

Entry
Database: PDB / ID: 9ea9
TitleCrystal structure of BoNT/A-NTNH-HA70 -VHH_F12-VHH_H7-Fab_NTNH complex
Components
  • (Nanobody ciA- ...) x 2
  • (anti-NTNH Fab) x 4
  • Botulinum neurotoxin type A
  • HA-70
  • HA70/A1
  • Non-toxic nonhemagglutinin type A
KeywordsTOXIN/IMMUNE SYSTEM / Botulinum neurotoxin / Progenitor toxin complex (PTC) / TOXIN / TOXIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated suppression of host exocytosis / ganglioside GT1b binding / Toxicity of botulinum toxin type A (botA) / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity ...symbiont-mediated suppression of host exocytosis / ganglioside GT1b binding / Toxicity of botulinum toxin type A (botA) / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / 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 / Hemagglutinin component HA-70, C-terminal / Haemagglutinin 70 C-terminal domain / Clostridium enterotoxin / Clostridium enterotoxin / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation 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 / 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 A / Non-toxic nonhemagglutinin type A / HA-70
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Vicugna pacos (alpaca)
Mus sp. (mice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsLam, K.H. / Gao, L. / Jin, R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI139087 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI158503 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI163178 United States
CitationJournal: Sci Adv / Year: 2025
Title: A nut-and-bolt assembly of the bimodular large progenitor botulinum neurotoxin complex.
Authors: Lam, K.H. / Gao, L. / Przykopanski, A. / Chen, B. / Huang, T. / Kruger, M. / Bartels, A.M. / Dorner, M.B. / Perry, K. / Dorner, B.G. / Rummel, A. / Jin, R.
History
DepositionNov 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Botulinum neurotoxin type A
B: Non-toxic nonhemagglutinin type A
C: Nanobody ciA-F12
F: Nanobody ciA-H7
I: HA-70
J: HA-70
D: HA-70
E: HA70/A1
G: HA-70
H: HA-70
K: anti-NTNH Fab
M: anti-NTNH Fab
N: anti-NTNH Fab
L: anti-NTNH Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)790,10835
Polymers788,83914
Non-polymers1,26921
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)203.650, 203.650, 479.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Components on special symmetry positions
IDModelComponents
11E-705-

MG

21E-706-

MG

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Components

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Protein , 4 types, 8 molecules ABIJDGHE

#1: Protein Botulinum neurotoxin type A / BoNT/A / Bontoxilysin-A / BOTOX / Botulinum neurotoxin type A1


Mass: 149479.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botA, atx, bonT / Production host: Escherichia coli (E. coli) / References: UniProt: P0DPI0
#2: Protein Non-toxic nonhemagglutinin type A / NTNHA / Botulinum neurotoxin type A non-toxic component


Mass: 138292.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: ant, ntnh, ACP52_06665 / Production host: Escherichia coli (E. coli) / References: UniProt: Q45914
#5: Protein
HA-70 / HA70


Mass: 71450.477 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: ha70 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KHU9
#6: Protein HA70/A1 / HA70


Mass: 71408.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: ha70 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KHU9

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Antibody , 6 types, 6 molecules CFKMNL

#3: Antibody Nanobody ciA-F12


Mass: 13698.003 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#4: Antibody Nanobody ciA-H7


Mass: 12989.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#7: Antibody anti-NTNH Fab


Mass: 11629.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus sp. (mice)
#8: Antibody anti-NTNH Fab


Mass: 12743.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus sp. (mice)
#9: Antibody anti-NTNH Fab


Mass: 9845.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus sp. (mice)
#10: Antibody anti-NTNH Fab


Mass: 11500.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus sp. (mice)

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Non-polymers , 4 types, 86 molecules

#11: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#12: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#13: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: Mg
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 61.01 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 1.1M ammonium sulfate, 0.1M Na acetate pH 5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.93→99.61 Å / Num. obs: 414819 / % possible obs: 99.87 % / Redundancy: 3.9 % / CC1/2: 0.994 / Net I/σ(I): 4.73
Reflection shellResolution: 2.93→3 Å / Num. unique obs: 47750 / CC1/2: 0.013 / % possible all: 99.95

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5107refinement
RAPDdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.93→99.61 Å / SU ML: 0.6447 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.16
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3084 1996 0.93 %
Rwork0.2864 213194 -
obs0.2867 215190 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.91 Å2
Refinement stepCycle: LAST / Resolution: 2.93→99.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39093 0 61 65 39219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003139948
X-RAY DIFFRACTIONf_angle_d0.599154238
X-RAY DIFFRACTIONf_chiral_restr0.04576013
X-RAY DIFFRACTIONf_plane_restr0.00397042
X-RAY DIFFRACTIONf_dihedral_angle_d14.795914631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.93-30.45521410.447515031X-RAY DIFFRACTION99.95
3-3.090.44031410.430415088X-RAY DIFFRACTION99.97
3.09-3.180.40731400.414515048X-RAY DIFFRACTION99.93
3.18-3.280.4041420.391615113X-RAY DIFFRACTION99.93
3.28-3.40.39631400.367715059X-RAY DIFFRACTION99.78
3.4-3.530.37081420.339715048X-RAY DIFFRACTION99.8
3.53-3.690.37221420.32715150X-RAY DIFFRACTION99.76
3.69-3.890.35981410.30115120X-RAY DIFFRACTION99.83
3.89-4.130.27371420.264115158X-RAY DIFFRACTION99.9
4.13-4.450.24321430.246715225X-RAY DIFFRACTION99.92
4.45-4.90.30451430.228415275X-RAY DIFFRACTION99.84
4.9-5.610.23091440.223615344X-RAY DIFFRACTION99.91
5.61-7.060.2641460.245615506X-RAY DIFFRACTION99.98
7.06-99.610.22931490.213516029X-RAY DIFFRACTION99.66

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