2QOG | pdb_00002qog

Crotoxin B, the basic PLA2 from Crotalus durissus terrificus.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 
    0.260 (Depositor) 
  • R-Value Work: 
    0.228 (Depositor) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Insights into the role of oligomeric state on the biological activities of crotoxin: crystal structure of a tetrameric phospholipase A2 formed by two isoforms of crotoxin B from Crotalus durissus terrificus venom.

Marchi-Salvador, D.P.Correa, L.C.Magro, A.J.Oliveira, C.Z.Soares, A.M.Fontes, M.R.

(2008) Proteins 72: 883-891

  • DOI: https://doi.org/10.1002/prot.21980
  • Primary Citation Related Structures: 
    2QOG

  • PubMed Abstract: 

    Crotoxin B (CB or Cdt PLA(2)) is a basic Asp49-PLA(2) found in the venom of Crotalus durissus terrificus and it is one of the subunits that constitute the crotoxin (Cro). This heterodimeric toxin, main component of the C. d. terrificus venom, is completed by an acidic, nontoxic, and nonenzymatic component (crotoxin A, CA or crotapotin), and it is related to important envenomation effects such as neurological disorders, myotoxicity, and renal failure. Although Cro has been crystallized since 1938, no crystal structure of this toxin or its subunits is currently available. In this work, the authors present the crystal structure of a novel tetrameric complex formed by two dimers of crotoxin B isoforms (CB1 and CB2). The results suggest that these assemblies are stable in solution and show that Ser1 and Glu92 of CB1 and CB2, respectively, play an important role in the oligomerization. The tetrameric and dimeric conformations resulting from the association of the isoforms may increase the neurotoxicity of the toxin CB by the creation of new binding sites, which could improve the affinity of the molecular complexes to the presynaptic membrane.


  • Organizational Affiliation
    • Departamento de Física e Biofísica, Instituto de Biociências, UNESP, Botucatu, SP, Brazil.

Macromolecule Content 

  • Total Structure Weight: 57.08 kDa 
  • Atom Count: 4,313 
  • Modeled Residue Count: 488 
  • Deposited Residue Count: 488 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phospholipase A2 CB2
A, D
122Crotalus durissus terrificusMutation(s): 0 
EC: 3.1.1.4
Membrane Entity: Yes 
UniProt
Find proteins for P24027 (Crotalus durissus terrificus)
Explore P24027 
Go to UniProtKB:  P24027
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24027
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Phospholipase A2 CB1
B, C
122Crotalus durissus terrificusMutation(s): 0 
EC: 3.1.1.4
Membrane Entity: Yes 
UniProt
Find proteins for P62022 (Crotalus durissus terrificus)
Explore P62022 
Go to UniProtKB:  P62022
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62022
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free:  0.260 (Depositor) 
  • R-Value Work:  0.228 (Depositor) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.895α = 90
b = 81.159β = 90
c = 100.039γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary