4ZCE | pdb_00004zce

Crystal Structure of the dust mite allergen Der p 23 from Dermatophagoides pteronyssinus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.190 (Depositor), 0.193 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4ZCE

This is version 1.5 of the entry. See complete history

Literature

Serological, genomic and structural analyses of the major mite allergen Der p 23.

Mueller, G.A.Randall, T.A.Glesner, J.Pedersen, L.C.Perera, L.Edwards, L.L.DeRose, E.F.Chapman, M.D.London, R.E.Pomes, A.

(2016) Clin Exp Allergy 46: 365-376

  • DOI: https://doi.org/10.1111/cea.12680
  • Primary Citation Related Structures: 
    4ZCE

  • PubMed Abstract: 

    Der p 23 was recently identified in a European population as a major allergen and potentially a chitin binding protein. This study sought to assess the importance of Der p 23 among other Dermatophagoides allergens in a North American population and to determine the structure for functional characterization. IgE binding to Der p 23, Der p 1, Der p 2, Der p 5, Der p 7 and Der p 8 was measured by ELISA. RNA-seq data from D. pteronyssinus were compared as estimates of allergen expression levels. The structure was analysed by X-ray crystallography and NMR. Despite a high prevalence of Der p 23, (75% vs. 87% and 79% for Der p 1 and Der p 2, respectively), the anti-Der p 23 IgE levels were relatively low. The patient response to the 6 allergens tested was variable (n = 47), but on average anti-Der p 1 and anti-Der p 2 together accounted for 85% of the specific IgE. In terms of abundance, the RNA expression level of Der p 23 is the lowest of the major allergens, thirty fold less than Der p 1 and sevenfold less than Der p 2. The structure of Der p 23 is a small, globular protein stabilized by two disulphide bonds, which is structurally related to allergens such as Blo t 12 that contain carbohydrate binding domains that bind chitin. Functional assays failed to confirm chitin binding by Der p 23. Der p 23 accounts for a small percentage of the IgE response to mite allergens, which is dominated by Der p 1 and Der p 2. The prevalence and amount of specific IgE to Der p 23 and Der p 2 are disproportionately high compared to the expression of other Dermatophagoides allergens.


  • Organizational Affiliation
    • Genome Integrity and Structural Biology Laboratory, Research Triangle Park, NC, USA.

Macromolecule Content 

  • Total Structure Weight: 11.95 kDa 
  • Atom Count: 1,024 
  • Modeled Residue Count: 96 
  • Deposited Residue Count: 100 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dust mite allergen
A, B
50Dermatophagoides pteronyssinusMutation(s): 0 
UniProt
Find proteins for L7N6F8 (Dermatophagoides pteronyssinus)
Explore L7N6F8 
Go to UniProtKB:  L7N6F8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL7N6F8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.190 (Depositor), 0.193 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 25.283α = 90
b = 53.519β = 95.47
c = 40.395γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesZ01-ES102885, ZIA-ES102645,R01AI077653

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2015-12-09
    Changes: Database references
  • Version 1.2: 2016-02-10
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.5: 2024-11-20
    Changes: Data collection, Database references, Structure summary