Crystal structure of Bermuda grass isoallergen BG60 provides insight into the various cross-allergenicity of the pollen group 4 allergens

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.220 

Starting Model: experimental
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Various cross-reactivity of the grass pollen group 4 allergens: crystallographic study of the Bermuda grass isoallergen Cyn d 4.

Huang, T.H.Peng, H.J.Su, S.N.Liaw, S.H.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1303-1310

  • DOI: https://doi.org/10.1107/S0907444912027552
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The structure of Cyn d 4, the group 4 allergen from Bermuda grass, is reported at 2.15 Å resolution and is the first crystal structure of a naturally isolated pollen allergen. A conserved N-terminal segment that is only present in the large isoallergens forms extensive interactions with surrounding residues and hence greatly enhances the structural stability of the protein. Cyn d 4 contains an FAD cofactor that is covalently linked to His88 and Cys152. To date, all identified bicovalent flavoproteins are oxidases and their substrates are either sugars or secondary metabolites. A deep large hydrophobic substrate-binding cleft is present. Thus, Cyn d 4 may be an oxidase that is involved in the biosynthesis of a pollen-specific metabolite. Cyn d 4 shares ~70% sequence identity with the Pooideae group 4 allergens. Various cross-reactivities between grass pollen group 4 allergens have previously been demonstrated using sera from allergic patients. The protein surface displays an unusually large number of positively charged clusters, reflecting the high pI of ~10. 38 decapeptides that cover the solvent-accessible sequences did not show any significant IgE-binding activity using sera with high Cyn d 4 reactivity from four patients, suggesting that the IgE epitopes of Cyn d 4 are predominantly conformational in nature. Several group 4 structures were then modelled and their potential cross-reactive and species-specific IgE epitopes were proposed.

  • Organizational Affiliation

    Department of Life Sciences, National Yang-Ming University, Taipei 11221, Taiwan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FAD-linked oxidoreductase BG60
A, B
497Cynodon dactylonMutation(s): 0 
Find proteins for Q5QJ60 (Cynodon dactylon)
Explore Q5QJ60 
Go to UniProtKB:  Q5QJ60
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5QJ60
Glycosylation Sites: 2
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
C, D
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.220 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.043α = 90
b = 86.043β = 90
c = 309.432γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-05
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary