2F08

Crystal structure of a major house dust mite allergen, Derf 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure and some properties of a major house dust mite allergen, Derf 2

Suzuki, M.Tanaka, Y.Korematsu, S.Mikami, B.Minato, N.

(2006) Biochem.Biophys.Res.Commun. 339: 679-686

  • DOI: 10.1016/j.bbrc.2005.11.065

  • PubMed Abstract: 
  • Pyroglyphid house dust mites are a major source of allergens in house dust. Mite allergens sensitize and induce asthma, rhinitis, and eczema in a large portion of patients with allergic diseases. Here, the crystal structure of a major mite allergen, ...

    Pyroglyphid house dust mites are a major source of allergens in house dust. Mite allergens sensitize and induce asthma, rhinitis, and eczema in a large portion of patients with allergic diseases. Here, the crystal structure of a major mite allergen, Derf 2, derived from Dermatophagoides farinae was solved by single isomorphous replacement method with anomalous scattering (SIRAS) at 2.1A resolution. The present study also demonstrated that the conformation of the allergen was critical in the determination of Th1/Th2 shift based on physicochemical and immunological analyses. This indicates that rigidly folded and singly dispersed structure is essentially required for the generation of Th2 type cells by the allergen, while conformational variant protein leads to Th1 skewing, irrespective of the same amino acid sequence. This structure/function relationship may allow us to develop a novel strategy for hyposensitization therapy in patients with allergic diseases triggered by house dust mite allergens.


    Organizational Affiliation

    Laboratory of Immunology and Cell Biology, Graduate School of Biostudies, Kyoto University, Yoshidakonoe-Cho, Sakyo-Ku, Kyoto 606-8501, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
mite allergen Der f II
A, B, C, D
129Dermatophagoides farinaeMutation(s): 0 
Gene Names: DERF2
Find proteins for Q00855 (Dermatophagoides farinae)
Go to UniProtKB:  Q00855
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P4C
Query on P4C

Download SDF File 
Download CCD File 
C
O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL
POLYETHYLENE 400
C14 H28 O8
CTLLATPOKUEFSQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 106.124α = 90.00
b = 54.328β = 91.35
c = 102.354γ = 90.00
Software Package:
Software NamePurpose
SAINTdata scaling
PHASESphasing
SAINTdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-11-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance