2VZN | pdb_00002vzn

Crystal structure of the major allergen from fire ant venom, Sol i 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 
    0.239 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Crystal Structure of the Major Allergen from Fire Ant Venom, Sol I 3

Padavattan, S.Schmidt, M.Hoffman, D.R.Markovic-Housley, Z.

(2008) J Mol Biology 383: 178

  • DOI: https://doi.org/10.1016/j.jmb.2008.08.023
  • Primary Citation Related Structures: 
    2VZN

  • PubMed Abstract: 

    Fire ant venom is an extremely potent allergy-inducing agent containing four major allergens, Sol i 1 to Sol i 4, which are the most frequent cause of hypersensitivity reactions to hymenoptera in the southern USA. The crystal structure of recombinant (Baculovirus) major fire ant allergen Sol i 3 has been determined to a resolution of 3.1 A by the method of molecular replacement. The secondary-structure elements of Sol i 3 are arranged in an alpha-beta-alpha sandwich fold consisting of a central antiparallel beta-sheet surrounded on both sides by alpha helices. The overall structure is very similar to that of the homologous wasp venom allergen Ves v 5 with major differences occurring in the solvent-exposed loop regions that contain amino acid insertions. Consequently, the limited conservation of surface chemical properties and topology between Sol i 3 and Ves v 5 may explain the observed lack of relevant cross-reactivity. It is concluded that Sol i 3 recognizes immunoglobulin E antibodies with a distinct set of its own epitopes, which are different from those of Ves v 5. Indeed, the molecular area in Sol i 3 covered by non-conserved residues is large enough to accommodate four unique Sol i 3 epitopes.


  • Organizational Affiliation
    • Department of Structural Biology, Biozentrum, University of Basel, CH-4056 Basel, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 49.65 kDa 
  • Atom Count: 3,219 
  • Modeled Residue Count: 420 
  • Deposited Residue Count: 436 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
VENOM ALLERGEN 3
A, B
218Solenopsis invictaMutation(s): 0 
UniProt
Find proteins for P35778 (Solenopsis invicta)
Explore P35778 
Go to UniProtKB:  P35778
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35778
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free:  0.239 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.355α = 90
b = 93.355β = 90
c = 144.051γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2019-05-15
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary