Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.11 kDa 
• Atom Count: 2210 
• Residue Count: 242 
• Unique protein chains: 1

3CXI

Structure of BthTX-I complexed with alpha-tocopherol

• DOI: 10.2210/pdb3CXI/pdb

• Classification: TOXIN
• Mutation(s): No 


• Deposited: 2008-04-24 Released: 2009-05-05 
• Deposition Author(s): dos Santos, J.I., Fontes, M.R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.243 
• R-Value Work: 0.195 

Literature

Comparative structural studies on Lys49-phospholipases A(2) from Bothrops genus reveal their myotoxic site.

dos Santos, J.I., Soares, A.M., Fontes, M.R.

(2009) J Struct Biol 167: 106-116

• PubMed: 19401234 
• DOI: 10.1016/j.jsb.2009.04.003
• Primary Citation of Related Structures:  
  2Q2J, 3CYL, 3CXI


• PubMed Abstract: 
  

Phospholipases A(2) (PLA(2)s) are membrane-associated enzymes that hydrolyze phospholipids at the sn-2 position, releasing lysophospholipids and free fatty acids. Phospholipase A(2) homologues (Lys49-PLA(2)s) are highly myotoxic and cause extensive tissue damage despite not showing measurable catalytic activity. They are found in different snake venoms and represent one third of bothropic venom composition. The importance of these toxins during envenomation is related to the pronounced local myotoxic effect they induce since this effect is not neutralized by serum therapy. We present herein three structures of Lys49-PLA(2)s from Bothrops genus snake venom crystallized under the same conditions, two of which were grown in the presence of alpha-tocopherol (vitamin E). Comparative structural analysis of these and other Lys49-PLA(2)s showed two different patterns of oligomeric conformation that are related to the presence or absence of ligands in the hydrophobic channel. This work also confirms the biological dimer indicated by recent studies in which both C-termini are in the dimeric interface. In this configuration, we propose that the myotoxic site of these toxins is composed by the Lys 20, Lys115 and Arg118 residues. For the first time, a residue from the short-helix (Lys20) is suggested as a member of this site and the importance of Tyr119 residue to myotoxicity of bothropic Lys49-PLA(2)s is also discussed. These results support a complete hypothesis for these PLA(2)s myotoxic activity consistent with all findings on bothropic Lys49-PLA(2)s studied up to this moment, including crystallographic, bioinformatics, biochemical and biophysical data.

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Organizational Affiliation: 

Depto. de Física e Biofísica, Instituto de Biociências, UNESP, SP, Brazil.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myotoxic phospholipase A2-like	A, B	121	N/A	Mutation(s): 0
Find proteins for Q90249 (Bothrops jararacussu) Explore Q90249  Go to UniProtKB:  Q90249

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VIT	A, B	VITAMIN E C29 H50 O2 GVJHHUAWPYXKBD-SYZUXVNWSA-N
PE4	B	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C16 H34 O8 PJWQOENWHPEPKI-UHFFFAOYSA-N
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.243 
• R-Value Work: 0.195 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.37	α = 90
b = 70.13	β = 102.23
c = 43.83	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-04-24 
• Released Date: 2009-05-05 
Deposition Author(s): dos Santos, J.I., Fontes, M.R.M.

Revision History 

• Version 1.0: 2009-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance