5G64

The complex between human IgE-Fc and two anti-IgE Fab fragments


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.715 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.259 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Allosteric mechanism of action of the therapeutic anti-IgE antibody omalizumab.

Davies, A.M.Allan, E.G.Keeble, A.H.Delgado, J.Cossins, B.P.Mitropoulou, A.N.Pang, M.O.Y.Ceska, T.Beavil, A.J.Craggs, G.Westwood, M.Henry, A.J.McDonnell, J.M.Sutton, B.J.

(2017) J. Biol. Chem. 292: 9975-9987

  • DOI: 10.1074/jbc.M117.776476

  • PubMed Abstract: 
  • Immunoglobulin E and its interactions with receptors FcϵRI and CD23 play a central role in allergic disease. Omalizumab, a clinically approved therapeutic antibody, inhibits the interaction between IgE and FcϵRI, preventing mast cell and basophil act ...

    Immunoglobulin E and its interactions with receptors FcϵRI and CD23 play a central role in allergic disease. Omalizumab, a clinically approved therapeutic antibody, inhibits the interaction between IgE and FcϵRI, preventing mast cell and basophil activation, and blocks IgE binding to CD23 on B cells and antigen-presenting cells. We solved the crystal structure of the complex between an omalizumab-derived Fab and IgE-Fc, with one Fab bound to each Cϵ3 domain. Free IgE-Fc adopts an acutely bent structure, but in the complex it is only partially bent, with large-scale conformational changes in the Cϵ3 domains that inhibit the interaction with FcϵRI. CD23 binding is inhibited sterically due to overlapping binding sites on each Cϵ3 domain. Studies of omalizumab Fab binding in solution demonstrate the allosteric basis for FcϵRI inhibition and, together with the structure, reveal how omalizumab may accelerate dissociation of receptor-bound IgE from FcϵRI, exploiting the intrinsic flexibility and allosteric potential of IgE.


    Organizational Affiliation

    the Medical Research Council and Asthma UK Centre in Allergic Mechanisms of Asthma, London SE1 1UL, and.,From the Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, james.mcdonnell@kcl.ac.uk.,From the Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, brian.sutton@kcl.ac.uk.,From the Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL.,UCB-Celltech, 208 Bath Road, Slough SL1 3WE, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IG EPSILON CHAIN C REGION
A, B
327N/AMutation(s): 2 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FAB FRAGMENT
H, I
230N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
FAB FRAGMENT
L, M
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

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

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.715 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.259 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 76.640α = 90.00
b = 231.190β = 90.00
c = 247.120γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-06-28
    Type: Data collection, Database references