6ZFM | pdb_00006zfm

Structure of alpha-Cobratoxin with a peptide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.4 of the entry. See complete history


Literature

Peptide Inhibitors of the alpha-Cobratoxin-Nicotinic Acetylcholine Receptor Interaction.

Lynagh, T.Kiontke, S.Meyhoff-Madsen, M.Gless, B.H.Johannesen, J.Kattelmann, S.Christiansen, A.Dufva, M.Laustsen, A.H.Devkota, K.Olsen, C.A.Kummel, D.Pless, S.A.Lohse, B.

(2020) J Med Chem 63: 13709-13718

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01202
  • Primary Citation of Related Structures:  
    6ZFM

  • PubMed Abstract: 

    Venomous snakebites cause >100 000 deaths every year, in many cases via potent depression of human neuromuscular signaling by snake α-neurotoxins. Emergency therapy still relies on antibody-based antivenom, hampered by poor access, frequent adverse reactions, and cumbersome production/purification. Combining high-throughput discovery and subsequent structure-function characterization, we present simple peptides that bind α-cobratoxin (α-Cbtx) and prevent its inhibition of nicotinic acetylcholine receptors (nAChRs) as a lead for the development of alternative antivenoms. Candidate peptides were identified by phage display and deep sequencing, and hits were characterized by electrophysiological recordings, leading to an 8-mer peptide that prevented α-Cbtx inhibition of nAChRs. We also solved the peptide:α-Cbtx cocrystal structure, revealing that the peptide, although of unique primary sequence, binds to α-Cbtx by mimicking structural features of the nAChR binding pocket. This demonstrates the potential of small peptides to neutralize lethal snake toxins in vitro, establishing a potential route to simple, synthetic, low-cost antivenoms.


  • Organizational Affiliation

    Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, 5008 Bergen, Norway.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-cobratoxin
A, B, D, E
71Naja kaouthiaMutation(s): 0 
UniProt
Find proteins for P01391 (Naja kaouthia)
Explore P01391 
Go to UniProtKB:  P01391
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01391
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
peptide 12
C, F
8Escherichia coli K-12Mutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.438α = 90
b = 49.438β = 90
c = 289.629γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted QJEClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyKU2531/2

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release
  • Version 1.1: 2020-12-09
    Changes: Database references
  • Version 1.2: 2020-12-23
    Changes: Structure summary
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-06
    Changes: Structure summary