4WTB

BthTX-I, a svPLA2s-like toxin, complexed with zinc ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Functional and structural studies of a Phospholipase A2-like protein complexed to zinc ions: Insights on its myotoxicity and inhibition mechanism.

Borges, R.J.Cardoso, F.F.Fernandes, C.A.Dreyer, T.R.de Moraes, D.S.Floriano, R.S.Rodrigues-Simioni, L.Fontes, M.R.

(2017) Biochim Biophys Acta 1861: 3199-3209

  • DOI: https://doi.org/10.1016/j.bbagen.2016.08.003
  • Primary Citation of Related Structures:  
    4WTB

  • PubMed Abstract: 

    One of the main challenges in snakebite envenomation treatment is the development of stable, versatile and efficient anti-venom therapies. Local myotoxicity in accidents involving snakes from the Bothrops genus is still a consequence of serum therapy inefficient neutralization that may lead to permanent sequelae in their victims. One of the classes of toxins that participate in muscle necrosis is the PLA 2 -like proteins. The aim of this work was to investigate the role of zinc ions in the inhibition of PLA 2 -like proteins and to advance the current knowledge of their action mechanism. Myographic and electrophysiological techniques were used to evaluate the inhibitory effect of zinc ions, isothermal titration calorimetry assays were used to measure the affinity between zinc ions and the toxin and X-ray crystallography was used to reveal details of this interaction. We demonstrated that zinc ions can effectively inhibit the toxin by the interaction with two different sites, which are related to two different mechanism of inhibition: preventing membrane disruption and impairing the toxin state transition. Furthermore, structural study presented here included an additional step in the current myotoxic mechanism improving the comprehension of the allosteric transition that PLA 2 -like proteins undergo to exert their function. Our findings show that zinc ions are inhibitors of PLA 2 -like proteins and suggest two different mechanisms of inhibition for these ions. Zinc is a new candidate that can assist in anti-venom treatments and can promote the design of new and even more accurate structure-based inhibitors for PLA 2 -like proteins.


  • Organizational Affiliation

    Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rua Prof. Dr. Antonio Celso Wagner Zanin, s/n, 18618-689 Botucatu, SP, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Basic phospholipase A2 homolog bothropstoxin-1
A, B
121Bothrops jararacussuMutation(s): 0 
UniProt
Find proteins for Q90249 (Bothrops jararacussu)
Explore Q90249 
Go to UniProtKB:  Q90249
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ90249
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.58α = 90
b = 56.58β = 90
c = 129.53γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil12/06502-5
Sao Paulo Research Foundation (FAPESP)Brazil09/12155-3
CAPESBrazil1592/2011

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2017-05-17
    Changes: Database references
  • Version 1.2: 2019-04-17
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-11-13
    Changes: Structure summary