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 6DKK | pdb_00006dkk

Structure of BoNT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.223 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6DKK

This is version 1.2 of the entry. See complete history. 

Literature

A viral-fusion-peptide-like molecular switch drives membrane insertion of botulinum neurotoxin A1.

Lam, K.H., Guo, Z., Krez, N., Matsui, T., Perry, K., Weisemann, J., Rummel, A., Bowen, M.E., Jin, R.

(2018) Nat Commun 9: 5367-5367

  • DOI: https://doi.org/10.1038/s41467-018-07789-4
  • Primary Citation Related Structures: 
    6DKK, 6MHJ

  • PubMed Abstract: 

    Botulinum neurotoxin (BoNT) delivers its protease domain across the vesicle membrane to enter the neuronal cytosol upon vesicle acidification. This process is mediated by its translocation domain (H N ), but the molecular mechanism underlying membrane insertion of H N remains poorly understood. Here, we report two crystal structures of BoNT/A1 H N that reveal a novel molecular switch (termed BoNT-switch) in H N , where buried α-helices transform into surface-exposed hydrophobic β-hairpins triggered by acidic pH. Locking the BoNT-switch by disulfide trapping inhibited the association of H N with anionic liposomes, blocked channel formation by H N , and reduced the neurotoxicity of BoNT/A1 by up to ~180-fold. Single particle counting studies showed that an acidic environment tends to promote BoNT/A1 self-association on liposomes, which is partly regulated by the BoNT-switch. These findings suggest that the BoNT-switch flips out upon exposure to the acidic endosomal pH, which enables membrane insertion of H N that subsequently leads to LC delivery.


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

Macromolecule Content 

  • Total Structure Weight: 75.1 kDa 
  • Atom Count: 5,176 
  • Modeled Residue Count: 639 
  • Deposited Residue Count: 654 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Botulinum neurotoxin type A
A, B
327Clostridium botulinum A str. ATCC 19397Mutation(s): 0 
Gene Names: botA, atx, bna
EC: 3.4.24.69
UniProt
Find proteins for P0DPI0 (Clostridium botulinum)
Explore P0DPI0 
Go to UniProtKB:  P0DPI0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DPI0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4

Query on PO4



Download:Ideal Coordinates CCD File
C [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.223 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.659α = 90
b = 167.659β = 90
c = 222.834γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI091823
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI125704
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21AI123920

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-26
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description