4IIS

Crystal structure of a glycosylated beta-1,3-glucanase (HEV B 2), An allergen from Hevea Brasiliensis (Space group P41)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6676 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structural analysis of the endogenous glycoallergen Hev b 2 (endo-beta-1,3-glucanase) from Hevea brasiliensis and its recognition by human basophils.

Rodriguez-Romero, A.Hernandez-Santoyo, A.Fuentes-Silva, D.Palomares, L.A.Munoz-Cruz, S.Yepez-Mulia, L.Orozco-Martinez, S.

(2014) Acta Crystallogr.,Sect.D 70: 329-341

  • DOI: 10.1107/S1399004713027673
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Endogenous glycosylated Hev b 2 (endo-β-1,3-glucanase) from Hevea brasiliensis is an important latex allergen that is recognized by IgE antibodies from patients who suffer from latex allergy. The carbohydrate moieties of Hev b 2 constitute a potentia ...

    Endogenous glycosylated Hev b 2 (endo-β-1,3-glucanase) from Hevea brasiliensis is an important latex allergen that is recognized by IgE antibodies from patients who suffer from latex allergy. The carbohydrate moieties of Hev b 2 constitute a potentially important IgE-binding epitope that could be responsible for its cross-reactivity. Here, the structure of the endogenous isoform II of Hev b 2 that exhibits three post-translational modifications, including an N-terminal pyroglutamate and two glycosylation sites at Asn27 and at Asn314, is reported from two crystal polymorphs. These modifications form a patch on the surface of the molecule that is proposed to be one of the binding sites for IgE. A structure is also proposed for the most important N-glycan present in this protein as determined by digestion with specific enzymes. To analyze the role of the carbohydrate moieties in IgE antibody binding and in human basophil activation, the glycoallergen was enzymatically deglycosylated and evaluated. Time-lapse automated video microscopy of basophils stimulated with glycosylated Hev b 2 revealed basophil activation and degranulation. Immunological studies suggested that carbohydrates on Hev b 2 represent an allergenic IgE epitope. In addition, a dimer was found in each asymmetric unit that may reflect a regulatory mechanism of this plant defence protein.


    Related Citations: 
    • Crystallization and identification of the glycosylated moieties of two isoforms of the main allergen Hev b 2 and preliminary X-ray analysis of two polymorphs of isoform II.
      Fuentes-Silva, D.,Mendoza-Hernandez, G.,Stojanoff, V.,Palomares, L.A.,Zenteno, E.,Torres-Larios, A.,Rodriguez-Romero, A.
      (2007) Acta Crystallogr.,Sect.F 63: 787


    Organizational Affiliation

    Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, CU, 04310 Coyoacán, DF, Mexico.,UMAE-Hospital de Pediatría, Centro Médico Nacional Siglo XXI, IMSS, Avenida Cuauhtémoc 330, Colonia Doctores, Mexico, DF, Mexico.,Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, 62250 Cuernavaca, MOR, Mexico.,Instituto Nacional de Pediatría, Insurgentes Sur 3700C, 04530 Cuicuilco, DF, Mexico.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-1,3-glucanase form 'RRII Gln 2'
A, B, C, D
316Hevea brasiliensisMutation(s): 0 
Find proteins for D1M8S7 (Hevea brasiliensis)
Go to UniProtKB:  D1M8S7
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CAC
Query on CAC

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Download CCD File 
A
CACODYLATE ION
dimethylarsinate
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
FLC
Query on FLC

Download SDF File 
Download CCD File 
A, D
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A, B, C, D
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6676 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.202 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 150.118α = 90.00
b = 150.118β = 90.00
c = 77.331γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHASERphasing
HKL-2000data collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-27
    Type: Initial release
  • Version 1.1: 2014-03-19
    Type: Database references
  • Version 2.0: 2019-12-25
    Type: Derived calculations, Polymer sequence