8HKH | pdb_00008hkh

Crystal structure of the LC/A1-DARPin18 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.306 (Depositor), 0.310 (DCC) 
  • R-Value Work: 
    0.262 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.264 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A DARPin promotes faster onset of botulinum neurotoxin A1 action.

Leka, O.Wu, Y.Zanetti, G.Furler, S.Reinberg, T.Marinho, J.Schaefer, J.V.Pluckthun, A.Li, X.Pirazzini, M.Kammerer, R.A.

(2023) Nat Commun 14: 8317-8317

  • DOI: https://doi.org/10.1038/s41467-023-44102-4
  • Primary Citation of Related Structures:  
    8HKH

  • PubMed Abstract: 

    In this study, we characterize Designed Ankyrin Repeat Proteins (DARPins) as investigative tools to probe botulinum neurotoxin A1 (BoNT/A1) structure and function. We identify DARPin-F5 that completely blocks SNAP25 substrate cleavage by BoNT/A1 in vitro. X-ray crystallography reveals that DARPin-F5 inhibits BoNT/A1 activity by interacting with a substrate-binding region between the α- and β-exosite. This DARPin does not block substrate cleavage of BoNT/A3, indicating that DARPin-F5 is a subtype-specific inhibitor. BoNT/A1 Glu-171 plays a critical role in the interaction with DARPin-F5 and its mutation to Asp, the residue found in BoNT/A3, results in a loss of inhibition of substrate cleavage. In contrast to the in vitro results, DARPin-F5 promotes faster substrate cleavage of BoNT/A1 in primary neurons and muscle tissue by increasing toxin translocation. Our findings could have important implications for the application of BoNT/A1 in therapeutic areas requiring faster onset of toxin action combined with long persistence.


  • Organizational Affiliation
    • Laboratory of Biomolecular Research, Division of Biology, Paul Scherrer Institut, 5232, Villigen PSI, Switzerland.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BoNT/A
A, B
436Clostridium botulinumMutation(s): 0 
Gene Names: a
UniProt
Find proteins for P0DPI1 (Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A))
Explore P0DPI1 
Go to UniProtKB:  P0DPI1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DPI1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Designed ankyrin repeat protein 18
C, D
149synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.306 (Depositor), 0.310 (DCC) 
  • R-Value Work:  0.262 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.264 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.56α = 74.98
b = 59.63β = 89.9
c = 102.18γ = 73.15
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_163449
Swiss National Science FoundationSwitzerland31003A_170028

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-29
    Type: Initial release
  • Version 1.1: 2025-01-01
    Changes: Database references, Structure summary