9GCN | pdb_00009gcn

Co-crystal VHH (TPL1158_01_C09) - alpha-cobratoxin (Naja kaouthia)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.292 (Depositor), 0.291 (DCC) 
  • R-Value Work: 
    0.238 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 
    0.243 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structural mechanisms behind the neutralisation of long-chain alpha-neurotoxins by broadly neutralising V H Hs discovered using a consensus antigen.

Damsbo, A.Burlet, N.J.Fernandez-Quintero, M.L.Benard-Valle, M.Overath, M.D.Guadarrama-Martinez, A.Vlamynck, A.Bisbo, I.Villalobos, C.Tulika, T.Alagon, A.Loeffler, J.R.Ward, A.B.Boddum, K.Morth, J.P.Rivera-de-Torre, E.Laustsen, A.H.

(2025) Commun Chem 8: 209-209

  • DOI: https://doi.org/10.1038/s42004-025-01600-4
  • Primary Citation Related Structures: 
    9GCN

  • PubMed Abstract: 

    Snakebite envenoming, a neglected tropical disease, affects millions globally, causing significant morbidity and mortality. Developing broadly neutralising monoclonal antibodies offers a promising approach to address the antigenic variation present in snake venoms. In this study, we designed a long-chain consensus α-neurotoxin, LCC, to serve as an antigen in a phage display-based antibody discovery campaign. Utilising a yeast expression system, we expressed LCC and identified 21 variable domains of heavy-chain-only antibodies (V H Hs) from immune libraries. These V H Hs were assessed for their binding affinity to various long-chain α-neurotoxins and their neutralising capability in vitro. The V H H with the broadest cross-reactivity and highest affinity, TPL1158_01_C09, was co-crystallised with α-cobratoxin to elucidate its binding mechanism. In vivo rodent studies demonstrated the neutralisation potential of TPL1158_01_C09. Our findings highlight that the use of a consensus toxin as an antigen coincided with the discovery of broadly neutralising V H Hs against snake venom toxins.


  • Organizational Affiliation
    • Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.

Macromolecule Content 

  • Total Structure Weight: 85.92 kDa 
  • Atom Count: 5,785 
  • Modeled Residue Count: 752 
  • Deposited Residue Count: 776 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein. Variable Domain of Heavy-Chain only Antibodies (VHH)A [auth D],
F [auth A],
G [auth B],
H [auth C]
123Vicugna pacosMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-cobratoxinB [auth Y],
C [auth V],
D [auth X],
E [auth Z]
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.292 (Depositor), 0.291 (DCC) 
  • R-Value Work:  0.238 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 0.243 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.37α = 90
b = 86.01β = 94.88
c = 75.92γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union850974
Wellcome TrustUnited Kingdom221702/Z/20/Z

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release
  • Version 1.1: 2025-08-13
    Changes: Derived calculations