8V13 | pdb_00008v13

Crystal structure of Black mamba toxin in complex with Centi-SNX-B03 antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.229 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

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


This is version 1.1 of the entry. See complete history


Literature

Snake venom protection by a cocktail of varespladib and broadly neutralizing human antibodies.

Glanville, J.Bellin, M.Pletnev, S.Zhang, B.Andrade, J.C.Kim, S.Tsao, D.Verardi, R.Bedi, R.Liao, S.Newland, R.Bayless, N.L.Youssef, S.Tully, E.S.Bylund, T.Kim, S.Hirou, H.Liu, T.Kwong, P.D.

(2025) Cell 188: 3117-3134.e11

  • DOI: https://doi.org/10.1016/j.cell.2025.03.050
  • Primary Citation of Related Structures:  
    8V13

  • PubMed Abstract: 

    Snake envenomation is a neglected tropical disease, with 600 species causing over 100,000 deaths and 300,000 permanent disabilities in humans annually. Broadly neutralizing antibodies and broad chemical inhibitors have been proposed as solutions, but how to develop a therapeutically effective cocktail and the number of required components have been unclear. To address this gap, we iteratively recovered two broadly neutralizing antivenom antibodies from the memory B cells of a hyperimmune human donor with extensive snake venom exposure. The antibodies recognized conserved neutralizing epitopes on prevalent long and short snake neurotoxins, with crystal structures revealing antibody mimicry of the interfaces between these neurotoxins and their host target, the nicotinic acetylcholine receptor. We combined and tested these antibodies and the phospholipase inhibitor varespladib. A 3-component cocktail rescued animals from whole-venom challenge of all species in a 19-member WHO Category 1 and Category 2 elapid diversity set, with complete protection against most snakes observed.


  • Organizational Affiliation
    • Centivax, Inc., 1 Tower Place, Suite 800, South San Francisco, CA 94080, USA. Electronic address: jake@centivax.com.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Centi-SNX-B03 Fab heavy chainA [auth H],
D [auth h]
230Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Centi-SNX-B03 Fab light chainB [auth L],
E [auth l]
215Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Short neurotoxin 1C [auth T],
F [auth t]
60Dendraspis polylepis polylepisMutation(s): 0 
UniProt
Find proteins for P01416 (Dendroaspis polylepis polylepis)
Explore P01416 
Go to UniProtKB:  P01416
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UniProt GroupP01416
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.229 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.539α = 90
b = 72.252β = 91.99
c = 179.656γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
BALBESphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited States--
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Database references