9CLP

Structure of ecarin from the venom of Kenyan saw-scaled viper in complex with the Fab of neutralizing antibody H11

  • Classification: HYDROLASE
  • Organism(s): Echis carinatus, Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2024-07-12 Released: 2024-09-11 
  • Deposition Author(s): Mindrebo, J.T., Lander, G.C.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), Wellcome Trust

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Importance of the Cysteine-Rich Domain of Snake Venom Prothrombin Activators: Insights Gained from Synthetic Neutralizing Antibodies.

Misson Mindrebo, L.E.Mindrebo, J.T.Tran, Q.Wilkinson, M.C.Smith, J.M.Verma, M.Casewell, N.R.Lander, G.C.Jardine, J.G.

(2024) Toxins (Basel) 16

  • DOI: https://doi.org/10.3390/toxins16080361
  • Primary Citation of Related Structures:  
    9CLP

  • PubMed Abstract: 

    Snake venoms are cocktails of biologically active molecules that have evolved to immobilize prey, but can also induce a severe pathology in humans that are bitten. While animal-derived polyclonal antivenoms are the primary treatment for snakebites, they often have limitations in efficacy and can cause severe adverse side effects. Building on recent efforts to develop improved antivenoms, notably through monoclonal antibodies, requires a comprehensive understanding of venom toxins. Among these toxins, snake venom metalloproteinases (SVMPs) play a pivotal role, particularly in viper envenomation, causing tissue damage, hemorrhage and coagulation disruption. One of the current challenges in the development of neutralizing monoclonal antibodies against SVMPs is the large size of the protein and the lack of existing knowledge of neutralizing epitopes. Here, we screened a synthetic human antibody library to isolate monoclonal antibodies against an SVMP from saw-scaled viper (genus Echis ) venom. Upon characterization, several antibodies were identified that effectively blocked SVMP-mediated prothrombin activation. Cryo-electron microscopy revealed the structural basis of antibody-mediated neutralization, pinpointing the non-catalytic cysteine-rich domain of SVMPs as a crucial target. These findings emphasize the importance of understanding the molecular mechanisms of SVMPs to counter their toxic effects, thus advancing the development of more effective antivenoms.


  • Organizational Affiliation

    Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc metalloproteinase-disintegrin-like ecarin426Echis carinatusMutation(s): 0 
EC: 3.4.24
UniProt
Find proteins for Q90495 (Echis carinatus)
Explore Q90495 
Go to UniProtKB:  Q90495
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UniProt GroupQ90495
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Endogenous peptideB [auth C]7Homo sapiensMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
H11 Fab heavy chainC [auth H]217Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
H11 Fab light chainD [auth L]217Homo sapiensMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesF32GM145143
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS095892
Wellcome TrustUnited Kingdom221705/Z/20/Z

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Structure summary