5G64

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.71 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.261 

wwPDB Validation   3D Report Full Report


This is version 2.0 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
  • Primary Citation of Related Structures:  
    5G64

  • 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 activation, and blocks IgE binding to CD23 on B cells and antigen-presenting cells ...

    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.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IG EPSILON CHAIN C REGIONA, B327Homo sapiensMutation(s): 2 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FAB FRAGMENTC [auth H],
D [auth I]
230Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
FAB FRAGMENTE [auth L],
F [auth M]
218Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth C],
H [auth D]
5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.71 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.261 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.64α = 90
b = 231.19β = 90
c = 247.12γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
MOLREPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary