7RJI

BthTX-II variant b, from Bothrops jararacussu venom, complexed with stearic acid

  • Classification: TOXIN
  • Organism(s): Bothrops jararacussu
  • Mutation(s): No 

  • Deposited: 2021-07-21 Released: 2022-01-05 
  • Deposition Author(s): Borges, R.J., Fontes, M.R.M.
  • Funding Organization(s): Sao Paulo Research Foundation (FAPESP), Brazilian National Council for Scientific and Technological Development (CNPq)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

BthTX-II from Bothrops jararacussu venom has variants with different oligomeric assemblies: An example of snake venom phospholipases A 2 versatility.

Borges, R.J.Salvador, G.H.M.Campanelli, H.B.Pimenta, D.C.de Oliveira Neto, M.Uson, I.Fontes, M.R.M.

(2021) Int J Biol Macromol 191: 255-266

  • DOI: 10.1016/j.ijbiomac.2021.09.083
  • Primary Citation of Related Structures:  
    7RJI, 7RJZ

  • PubMed Abstract: 
  • Phospholipases A 2 (PLA 2 s) are found in almost every venomous snake family. In snakebites, some PLA 2 s can quickly cause local myonecrosis, which may lead to permanent sequelae if antivenom is administered belatedly. They hydrolyse phospholipids in membranes through a catalytic calcium ions-dependent mechanism ...

    Phospholipases A 2 (PLA 2 s) are found in almost every venomous snake family. In snakebites, some PLA 2 s can quickly cause local myonecrosis, which may lead to permanent sequelae if antivenom is administered belatedly. They hydrolyse phospholipids in membranes through a catalytic calcium ions-dependent mechanism. BthTX-II is a basic PLA 2 and the second major component in the venom of Bothrops jararacussu. Herein, using the software SEQUENCE SLIDER, which integrates crystallographic, mass spectrometry and genetic data, we characterized the primary, tertiary and quaternary structure of two BthTX-II variants (called a and b), which diverge in 7 residues. Crystallographic structure BthTX-IIa is in a Tense-state with its distorted calcium binding loop buried in the dimer interface, contrarily, the novel BthTX-IIb structure is a monomer in a Relax-state with a fatty acid in the hydrophobic channel. Structural data in solution reveals that both variants are monomeric in neutral physiological conditions and mostly dimeric in an acidic environment, being catalytic active in both situations. Therefore, we propose two myotoxic mechanisms for BthTX-II, a catalytic one associated with the monomeric assembly, whereas the other has a calcium independent activity related to its C-terminal region, adopting a dimeric conformation similar to PLA 2 -like proteins.


    Organizational Affiliation

    Department of Biophysics and Pharmacology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, São Paulo 18618-689, Brazil. Electronic address: marcos.fontes@unesp.br.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BthTX-IIbA122Bothrops jararacussuMutation(s): 0 
EC: 3.1.1.4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
STE (Subject of Investigation/LOI)
Query on STE

Download Ideal Coordinates CCD File 
B [auth A]STEARIC ACID
C18 H36 O2
QIQXTHQIDYTFRH-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A], E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.036α = 90
b = 83.036β = 90
c = 124.83γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil16/24191-8
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil302883/2017-7

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-05
    Type: Initial release