4GRG

Crystal structure of IgE complexed with E2_79, an anti-IgE inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.24 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.270 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Accelerated disassembly of IgE-receptor complexes by a disruptive macromolecular inhibitor.

Kim, B.Eggel, A.Tarchevskaya, S.S.Vogel, M.Prinz, H.Jardetzky, T.S.

(2012) Nature 491: 613-617

  • DOI: 10.1038/nature11546

  • PubMed Abstract: 
  • IgE antibodies bind the high-affinity IgE Fc receptor (FcεRI), found primarily on mast cells and basophils, and trigger inflammatory cascades of the allergic response. Inhibitors of IgE-FcεRI binding have been identified and an anti-IgE therapeutic a ...

    IgE antibodies bind the high-affinity IgE Fc receptor (FcεRI), found primarily on mast cells and basophils, and trigger inflammatory cascades of the allergic response. Inhibitors of IgE-FcεRI binding have been identified and an anti-IgE therapeutic antibody (omalizumab) is used to treat severe allergic asthma. However, preformed IgE-FcεRI complexes that prime cells before allergen exposure dissociate extremely slowly and cannot be disrupted by strictly competitive inhibitors. IgE-Fc conformational flexibility indicated that inhibition could be mediated by allosteric or other non-classical mechanisms. Here we demonstrate that an engineered protein inhibitor, DARPin E2_79 (refs 9, 10, 11), acts through a non-classical inhibition mechanism, not only blocking IgE-FcεRI interactions, but actively stimulating the dissociation of preformed ligand-receptor complexes. The structure of the E2_79-IgE-Fc(3-4) complex predicts the presence of two non-equivalent E2_79 sites in the asymmetric IgE-FcεRI complex, with site 1 distant from the receptor and site 2 exhibiting partial steric overlap. Although the structure is indicative of an allosteric inhibition mechanism, mutational studies and quantitative kinetic modelling indicate that E2_79 acts through a facilitated dissociation mechanism at site 2 alone. These results demonstrate that high-affinity IgE-FcεRI complexes can be actively dissociated to block the allergic response and suggest that protein-protein complexes may be more generally amenable to active disruption by macromolecular inhibitors.


    Organizational Affiliation

    Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ANTI-IGE INHIBITOR E2_79
A, B
135Escherichia coliN/A
Find proteins for L7MTK7 (Escherichia coli)
Go to UniProtKB:  L7MTK7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ig epsilon chain C region
C, D
230Homo sapiensGene Names: IGHE
Find proteins for P01854 (Homo sapiens)
Go to UniProtKB:  P01854
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.24 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.270 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 71.315α = 90.00
b = 71.315β = 90.00
c = 178.520γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASESphasing
HKL-2000data scaling
HKL-2000data reduction
HKL-2000data collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-12
    Type: Initial release