Crystal structure of nontoxic nonhemagglutinin subcomponent (NTNHA) from clostridium botulinum serotype D strain 4947

Experimental Data Snapshot

  • Resolution: 3.90 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.231 

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Small-angle X-ray scattering reveals structural dynamics of the botulinum neurotoxin associating protein, nontoxic nonhemagglutinin

Sagane, Y.Miyashita, S.Miyata, K.Matsumoto, T.Inui, K.Hayashi, S.Suzuki, T.Hasegawa, K.Yajima, S.Yamano, A.Niwa, K.Watanabe, T.

(2012) Biochem Biophys Res Commun 425: 256-260

  • DOI: https://doi.org/10.1016/j.bbrc.2012.07.077
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    In cell culture supernatants, the botulinum neurotoxin (BoNT) exists as part of a toxin complex (TC) in which nontoxic nonhemagglutinin (NTNHA) and/or hemagglutinins (HAs) are assembled onto the BoNT. A series of investigations indicated that formation of the TC is vital for delivery of the toxin to nerve cells through the digestive tract. In the assembly process, BoNT binds to NTNHA yielding M-TC, and it then matures into L-TC by further association with the HAs via NTNHA in the M-TC. Here, we report a crystal structure of the NTNHA from Clostridium botulinum serotype D strain 4947. Additionally, we performed small-angle X-ray scattering (SAXS) analysis of the NTNHA and the M-TC to elucidate the solution structure. The crystal structure of D-4947 NTNHA revealed that BoNT and NTNHA share a closely related structure consisting of three domains. The SAXS image indicated that, even though the N-terminal two-thirds of the NTNHA molecule had an apparently similar conformation in both the crystal and solution structures, the C-terminal third of the molecule showed a more extended structure in the SAXS image than that seen in the crystallographic image. The discrepancy between the crystal and solution structures implies a high flexibility of the C-terminal third domain of NTNHA, which is involved in binding to BoNT. Structural dynamics of the NTNHA molecule revealed by SAXS may explain its binding to BoNT to form the BoNT/NTNHA complex.

  • Organizational Affiliation

    Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493, Japan.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NTNHA1,196Clostridium botulinumMutation(s): 0 
Gene Names: ntnha
Find proteins for Q9LBR2 (Clostridium botulinum D phage)
Explore Q9LBR2 
Go to UniProtKB:  Q9LBR2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LBR2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.90 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.231 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.851α = 90
b = 147.851β = 90
c = 229.741γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-19
    Type: Initial release