3EBW | pdb_00003ebw

Crystal structure of major allergens, Per a 4 from cockroaches


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.276 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.231 (Depositor), 0.247 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3EBW

This is version 1.3 of the entry. See complete history

Literature

Structures of two major allergens, Bla g 4 and Per a 4, from cockroaches and their IgE binding epitopes.

Tan, Y.W.Chan, S.L.Ong, T.C.Yit, L.Y.Tiong, Y.S.Chew, F.T.Sivaraman, J.Mok, Y.K.

(2008) J Biological Chem 284: 3148-3157

  • DOI: https://doi.org/10.1074/jbc.M807209200
  • Primary Citation Related Structures: 
    3EBK, 3EBW

  • PubMed Abstract: 

    Inhalant allergens from cockroaches are an important cause of asthma to millions of individuals worldwide. Here we report for the first time the structures of two major cockroach allergens, Bla g 4 and Per a 4, that adopt a typical lipocalin fold but with distinct structural features as compared with other known lipocalin allergens. Both Bla g 4 and Per a 4 contain two long-range disulfide bonds linking the N and C termini to a beta-barrel. The C-terminal helix of Bla g 4 is bent and greatly extended toward the N terminus. Bla g 4 is found to be a monomer, whereas Per a 4 exists as a dimer in solution with a novel dimeric interface involving residues from loops at the top and bottom of the beta-barrel. Putative ligand binding sites of both allergens are determined by docking of the juvenile hormone III inside the beta-barrel and found to interact with the ligand using non-conserved residues. Bla g 4 and Per a 4 are found to be cross-reactive in sera IgE binding, at least in the Singaporean Chinese population tested. A major IgE binding epitope unique to Per a 4 is found on the loops at the bottom of the beta-barrel that may aid the development of hypoallergens for immunotherapy.


  • Organizational Affiliation
    • Department of Biological Sciences, National University of Singapore, Singapore 17543.

Macromolecule Content 

  • Total Structure Weight: 38.15 kDa 
  • Atom Count: 2,560 
  • Modeled Residue Count: 314 
  • Deposited Residue Count: 326 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Per a 4 allergen
A, B
163Periplaneta americanaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q1M0Y5 (Periplaneta americana)
Explore Q1M0Y5 
Go to UniProtKB:  Q1M0Y5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1M0Y5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PE4

Query on PE4



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.276 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.231 (Depositor), 0.247 (DCC) 
Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.985α = 90
b = 62.985β = 90
c = 143.699γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary