9RIU | pdb_00009riu

Co-crystal of broadly neutralizing VHH in complex with short neurotoxin 1 (P01426) Naja pallida


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.361 (Depositor), 0.360 (DCC) 
  • R-Value Work: 
    0.324 (Depositor), 0.324 (DCC) 
  • R-Value Observed: 
    0.326 (Depositor) 

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


This is version 1.2 of the entry. See complete history


Literature

Nanobody-based recombinant antivenom for cobra, mamba and rinkhals bites.

Ahmadi, S.Burlet, N.J.Benard-Valle, M.Guadarrama-Martinez, A.Kerwin, S.Cardoso, I.A.Marriott, A.E.Edge, R.J.Crittenden, E.Neri-Castro, E.Fernandez-Quintero, M.L.Nguyen, G.T.T.O'Brien, C.Wouters, Y.Kalogeropoulos, K.Thumtecho, S.Ebersole, T.W.Dahl, C.H.Glegg-Sorensen, E.U.Jansen, T.Boddum, K.Manousaki, E.Rivera-de-Torre, E.Ward, A.B.Morth, J.P.Alagon, A.Mackessy, S.P.Ainsworth, S.Menzies, S.K.Casewell, N.R.Jenkins, T.P.Ljungars, A.Laustsen, A.H.

(2025) Nature 647: 716-725

  • DOI: https://doi.org/10.1038/s41586-025-09661-0
  • Primary Citation of Related Structures:  
    9RIT, 9RIU

  • PubMed Abstract: 

    Each year, snakebite envenoming claims thousands of lives and causes severe injury to victims across sub-Saharan Africa, many of whom depend on antivenoms derived from animal plasma as their sole treatment option 1 . Traditional antivenoms are expensive, can cause adverse immunological reactions, offer limited efficacy against local tissue damage and are often ineffective against all medically relevant snake species 2 . There is thus an urgent unmet medical need for innovation in snakebite envenoming therapy. However, developing broad-spectrum treatments is highly challenging owing to the vast diversity of venomous snakes and the complex and variable composition of their venoms 3 . Here we addressed this challenge by immunizing an alpaca and a llama with the venoms of 18 different snakes, including mambas, cobras and a rinkhals, constructing phage display libraries, and identifying high-affinity broadly neutralizing nanobodies. We combined eight of these nanobodies into a defined oligoclonal mixture, resulting in an experimental polyvalent recombinant antivenom that was capable of neutralizing seven toxin families or subfamilies. This antivenom effectively prevented venom-induced lethality in vivo across 17 African elapid snake species and markedly reduced venom-induced dermonecrosis for all tested cytotoxic venoms. The recombinant antivenom performed better than a currently used plasma-derived antivenom and therefore shows considerable promise for comprehensive, continent-wide protection against snakebites by all medically relevant African elapids.


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

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Variable Domain of Heavy-Chain only Antibody (VHH)
A, C
129Vicugna pacosMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Short neurotoxin 1
B, D
61Naja pallidaMutation(s): 0 
UniProt
Find proteins for P01426 (Naja pallida)
Explore P01426 
Go to UniProtKB:  P01426
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01426
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth C],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
S [auth D],
T [auth D]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.361 (Depositor), 0.360 (DCC) 
  • R-Value Work:  0.324 (Depositor), 0.324 (DCC) 
  • R-Value Observed: 0.326 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.15α = 90
b = 104.09β = 90
c = 79.34γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

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
Novo Nordisk FoundationDenmarkNNF24OC0088714

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-05
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Database references
  • Version 1.2: 2025-12-03
    Changes: Database references