6TMY | pdb_00006tmy

Crystal structure of isoform CBd of the basic phospholipase A2 subunit of crotoxin from Crotalus durissus terrificus

• PDB DOI: https://doi.org/10.2210/pdb6TMY/pdb

• Classification: HYDROLASE
• Organism(s): Crotalus durissus terrificus
• Mutation(s): No 


• Deposited: 2019-12-05 Released: 2020-12-02 
• Deposition Author(s): Nemecz, D., Ostrowski, M., Saul, F.A., Faure, G.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.214 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.192 (Depositor) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Isoform CBd of the Basic Phospholipase A 2 Subunit of Crotoxin: Description of the Structural Framework of CB for Interaction with Protein Targets.

Nemecz, D., Ostrowski, M., Ravatin, M., Saul, F., Faure, G.

(2020) Molecules 25

• PubMed: 33202772 
• DOI: https://doi.org/10.3390/molecules25225290
• Primary Citation Related Structures: 
  6TMY


• PubMed Abstract: 
  

  Crotoxin, from the venom of the South American rattlesnake Crotalus durissus terrificus, is a potent heterodimeric presynaptic β-neurotoxin that exists in individual snake venom as a mixture of isoforms of a basic phospholipase A ₂ (PLA ₂ ) subunit (CBa ₂ , CBb, CBc, and CBd) and acidic subunit (CA _1-4 ). Specific natural mutations in CB isoforms are implicated in functional differences between crotoxin isoforms. The three-dimensional structure of two individual CB isoforms (CBa ₂ , CBc), and one isoform in a crotoxin (CA ₂ CBb) complex, have been previously reported. This study concerns CBd, which by interaction with various protein targets exhibits many physiological or pharmacological functions. It binds with high affinity to presynaptic receptors showing neurotoxicity, but also interacts with human coagulation factor Xa (hFXa), exhibiting anticoagulant effect, and acts as a positive allosteric modulator and corrector of mutated chloride channel, cystic fibrosis transmembrane conductance regulator (CFTR), implicated in cystic fibrosis. Thus, CBd represents a novel family of agents that have potential in identifying new drug leads related to anticoagulant and anti-cystic fibrosis function. We determined here the X-ray structure of CBd and compare it with the three other natural isoforms of CB. The structural role of specific amino acid variations between CB isoforms are analyzed and the structural framework of CB for interaction with protein targets is described.

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Organizational Affiliation: 
• Institut Pasteur, Récepteurs-Canaux, CNRS UMR 3571, Département de Neuroscience, 25, rue du Dr. Roux, F-75015 Paris, France.
Biochemistry Department, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland.
Sanofi R&D, Integrated Drug Discovery-High Content Biology, 94400 Vitry-sur-Seine, France.
Institut Pasteur, Plateforme de Cristallographie-C2RT, CNRS UMR 3528, 75015 Paris, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 88.73 kDa 
• Atom Count: 6,853 
• Modeled Residue Count: 732 
• Deposited Residue Count: 732 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipase A2 crotoxin basic subunit CBc	A, B, C, D, E, F	122	Crotalus durissus terrificus	Mutation(s): 0  EC: 3.1.1.4
UniProt
Find proteins for C0HM14 (Crotalus durissus terrificus) Explore C0HM14  Go to UniProtKB:  C0HM14

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	BA [auth E], DA [auth E], H [auth A], HA [auth F], I [auth A], IA [auth F], JA [auth F], O [auth B], P [auth B], S [auth C], T [auth C], U [auth C], Y [auth D]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
CL	EA [auth E], J [auth A], K [auth A], KA [auth F], L [auth A], V [auth C], Z [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	AA [auth D], CA [auth E], FA [auth E], G [auth A], GA [auth F], LA [auth F], M [auth A], N [auth B], Q [auth B], R [auth C], W [auth C], X [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.214 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.192 (Depositor) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.626	α = 90
b = 75.592	β = 121.85
c = 109.012	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-02 
Deposition Author(s): Nemecz, D., Ostrowski, M., Saul, F.A., Faure, G.

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Funding Organization	Location	Grant Number
Other government	Poland	POKL.04.01.01-00-081/10

Revision History  

• Version 1.0: 2020-12-02
  Type: Initial release
  
• Version 1.1: 2020-12-09
  Changes: Derived calculations
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary