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 9EA9 | pdb_00009ea9

Crystal structure of BoNT/A-NTNH-HA70 -VHH_F12-VHH_H7-Fab_NTNH complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free: 
    0.308 (Depositor), 0.308 (DCC) 
  • R-Value Work: 
    0.286 (Depositor), 0.287 (DCC) 
  • R-Value Observed: 
    0.287 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history. 

Literature

A nut-and-bolt assembly of the bimodular large progenitor botulinum neurotoxin complex.

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.

(2025) Sci Adv 11: eadx5831

  • DOI: https://doi.org/10.1126/sciadv.adx5831
  • Primary Citation Related Structures: 
    9EA9

  • PubMed Abstract: 

    Botulinum neurotoxin serotype A (BoNT/A) is naturally produced by bacteria along with four nontoxic neurotoxin-associated proteins (NTNH, HA70, HA33, and HA17), forming a bimodular large progenitor toxin complex (L-PTC). The BoNT/A-NTNH complex protects the toxin from adverse environment, while the complex consisting of HA proteins facilitates toxin absorption during oral intoxication. How these two independent modules assemble into the L-PTC remains unclear. Here, we report the crystal structure of the BoNT/A-NTNH-HA70 complex at ~2.9-Å resolution. The structure reveals that the BoNT/A-NTNH complex is anchored into a concentric double β-barrel channel of trimeric HA70 through a short β-hairpin of NTNH (termed nLoop), resembling a nut-and-bolt attachment. We find that the nLoop of NTNH is strictly conserved across HA-containing BoNT complexes and that NTNH-HA70 binding is interchangeable among them. Furthermore, we demonstrate that the nLoop functions as a minimal motif enabling attachment of a protein-of-interest to the HA complex, with potential applications in oral biologics delivery.


  • Organizational Affiliation: 
    • Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA.

Macromolecule Content 

  • Total Structure Weight: 790.11 kDa 
  • Atom Count: 39,218 
  • Modeled Residue Count: 4,888 
  • Deposited Residue Count: 6,914 
  • Unique protein chains: 10

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Botulinum neurotoxin type A1,296Clostridium botulinumMutation(s): 1 
Gene Names: botA, atx, bonT
UniProt
Find proteins for P0DPI0 (Clostridium botulinum)
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UniProt GroupP0DPI0
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Non-toxic nonhemagglutinin type A1,194Clostridium botulinumMutation(s): 0 
Gene Names: ant, ntnh, ACP52_06665
UniProt
Find proteins for Q45914 (Clostridium botulinum)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody ciA-F12128Vicugna pacosMutation(s): 0 
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody ciA-H7D [auth F]121Vicugna pacosMutation(s): 0 
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
HA-70E [auth I],
F [auth J],
G [auth D],
I [auth G],
J [auth H]
626Clostridium botulinumMutation(s): 0 
Gene Names: ha70
UniProt
Find proteins for Q8KHU9 (Clostridium botulinum)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
HA70/A1H [auth E]626Clostridium botulinumMutation(s): 0 
Gene Names: ha70
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Find proteins for Q8KHU9 (Clostridium botulinum)
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UniProt GroupQ8KHU9
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
anti-NTNH Fab105Mus sp.Mutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
anti-NTNH FabL [auth M]117Mus sp.Mutation(s): 0 
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
anti-NTNH FabM [auth N]94Mus sp.Mutation(s): 0 
UniProt
Find proteins for P01863 (Mus musculus)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
anti-NTNH FabN [auth L]103Mus sp.Mutation(s): 0 
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
AA [auth D]
BA [auth E]
O [auth A]
P [auth A]
Q [auth A]
AA [auth D],
BA [auth E],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
U [auth B],
V [auth B],
W [auth B],
X [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN

Query on ZN



Download:Ideal Coordinates CCD File
S [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
CA [auth E]
DA [auth E]
EA [auth E]
FA [auth E]
GA [auth E]
CA [auth E],
DA [auth E],
EA [auth E],
FA [auth E],
GA [auth E],
HA [auth E],
IA [auth H],
T [auth A],
Y [auth B],
Z [auth J]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.93 Å
  • R-Value Free:  0.308 (Depositor), 0.308 (DCC) 
  • R-Value Work:  0.286 (Depositor), 0.287 (DCC) 
  • R-Value Observed: 0.287 (Depositor) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 203.65α = 90
b = 203.65β = 90
c = 479.91γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
RAPDdata reduction
pointlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI139087
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI158503
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21AI163178

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-17
    Type: Initial release