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


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 of 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.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Botulinum neurotoxin type A1,296Clostridium botulinumMutation(s): 1 
Gene Names: botAatxbonT
UniProt
Find proteins for P0DPI0 (Clostridium botulinum)
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UniProt GroupP0DPI0
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Non-toxic nonhemagglutinin type A1,194Clostridium botulinumMutation(s): 0 
Gene Names: antntnhACP52_06665
UniProt
Find proteins for Q45914 (Clostridium botulinum)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody ciA-F12128Vicugna pacosMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody ciA-H7D [auth F]121Vicugna pacosMutation(s): 0 
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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
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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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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
anti-NTNH Fab105Mus sp.Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
anti-NTNH FabL [auth M]117Mus sp.Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
anti-NTNH FabM [auth N]94Mus sp.Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
anti-NTNH FabN [auth L]103Mus sp.Mutation(s): 0 
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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

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S [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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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