1XWV | pdb_00001xwv

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

• PDB DOI: https://doi.org/10.2210/pdb1XWV/pdb

• Classification: ALLERGEN
• Organism(s): Dermatophagoides farinae
• Expression System: Komagataella pastoris
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2004-11-02 Released: 2004-12-14 
• Deposition Author(s): Johannessen, B.R., Skov, L.K., Kastrup, J.S., Kristensen, O., Bolwig, C., Larsen, J.N., Spangfort, M., Lund, K., Gajhede, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.257 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

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

• PubMed: 15710415 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.2 kDa 
• Atom Count: 2,329 
• Modeled Residue Count: 258 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Der f II	A, B	129	Dermatophagoides farinae	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q00855 (Dermatophagoides farinae) Explore Q00855  Go to UniProtKB:  Q00855

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE3	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	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 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.712	α = 85.98
b = 47.638	β = 75.9
c = 48.275	γ = 82.76

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-14 
Deposition Author(s): Johannessen, B.R., Skov, L.K., Kastrup, J.S., Kristensen, O., Bolwig, C., Larsen, J.N., Spangfort, M., Lund, K., Gajhede, M.

Revision History  

• 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