4GT7

An engineered disulfide bond reversibly traps the IgE-Fc3-4 in a closed, non-receptor binding conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An engineered disulfide bond reversibly traps the IgE-Fc3-4 in a closed, nonreceptor binding conformation.

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

(2012) J.Biol.Chem. 287: 36251-36257

  • DOI: 10.1074/jbc.M112.407502

  • PubMed Abstract: 
  • IgE antibodies interact with the high affinity IgE Fc receptor, FcεRI, and activate inflammatory pathways associated with the allergic response. The IgE-Fc region, comprising the C-terminal domains of the IgE heavy chain, binds FcεRI and can adopt di ...

    IgE antibodies interact with the high affinity IgE Fc receptor, FcεRI, and activate inflammatory pathways associated with the allergic response. The IgE-Fc region, comprising the C-terminal domains of the IgE heavy chain, binds FcεRI and can adopt different conformations ranging from a closed form incompatible with receptor binding to an open, receptor-bound state. A number of intermediate states are also observed in different IgE-Fc crystal forms. To further explore this apparent IgE-Fc conformational flexibility and to potentially trap a closed, inactive state, we generated a series of disulfide bond mutants. Here we describe the structure and biochemical properties of an IgE-Fc mutant that is trapped in the closed, non-receptor binding state via an engineered disulfide at residue 335 (Cys-335). Reduction of the disulfide at Cys-335 restores the ability of IgE-Fc to bind to its high affinity receptor, FcεRIα. The structure of the Cys-335 mutant shows that its conformation is within the range of previously observed, closed form IgE-Fc structures and that it retains the hydrophobic pocket found in the hinge region of the closed conformation. Locking the IgE-Fc into the closed state with the Cys-335 mutation does not affect binding of two other IgE-Fc ligands, omalizumab and DARPin E2_79, demonstrating selective blocking of the high affinity receptor binding.


    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
Ig epsilon chain C region
A, B, C, D
221Homo sapiensMutation(s): 1 
Gene Names: IGHE
Find proteins for P01854 (Homo sapiens)
Go to UniProtKB:  P01854
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B, C, D
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B, C, D
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 106.753α = 90.00
b = 104.807β = 94.51
c = 45.899γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-12
    Type: Initial release
  • Version 1.1: 2013-01-02
    Type: Database references