1XWV

Structure of the house dust mite allergen Der f 2: Implications for function and molecular basis of IgE cross-reactivity

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history. 


Literature

Structure of the house dust mite allergen Der f 2: implications for function and molecular basis of IgE cross-reactivity.

Johannessen, B.R., Skov, L.K., Kastrup, J.S., Kristensen, O., Bolwig, C., Larsen, J.N., Spangfort, M., Lund, K., Gajhede, M.

(2005) FEBS Lett 579: 1208-1212

  • DOI: https://doi.org/10.1016/j.febslet.2004.11.115
  • Primary Citation of Related Structures:  
    1XWV

  • PubMed Abstract: 

    The X-ray structure of the group 2 major allergen from Dermatophagoides farinae (Der f 2) was determined to 1.83 A resolution. The overall Der f 2 structure comprises a single domain of immunoglobulin fold with two anti-parallel beta-sheets. A large hydrophobic cavity is formed in the interior of Der f 2. Structural comparisons to distantly related proteins suggest a role in lipid binding. Immunoglobulin E (IgE) cross-reactivity between group 2 house dust mite major allergens can be explained by conserved surface areas representing IgE binding epitopes.

    • Organizational Affiliation: 

    Biostructural Research, Department of Medicinal Chemistry, Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen, Denmark.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Der f II
A, B
129Dermatophagoides farinaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q00855 (Dermatophagoides farinae)
Explore Q00855 
Go to UniProtKB:  Q00855
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00855
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PE3
Query on PE3
Download Ideal Coordinates CCD File 
C [auth A]3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL
C28 H58 O15
ILLKMACMBHTSHP-UHFFFAOYSA-N
XPE
Query on XPE
Download Ideal Coordinates CCD File 
D [auth B]3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL
C20 H42 O11
DTPCFIHYWYONMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 25.712α = 85.98
b = 47.638β = 75.9
c = 48.275γ = 82.76
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
CNSrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-06
    Changes: Structure summary