5LGK

Crystal structure of the human IgE-Fc bound to its B cell receptor derCD23


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.267 

wwPDB Validation 3D Report Full Report



Literature

IgE binds asymmetrically to its B cell receptor CD23.

Dhaliwal, B.Pang, M.O.Keeble, A.H.James, L.K.Gould, H.J.McDonnell, J.M.Sutton, B.J.Beavil, A.J.

(2017) Sci Rep 7: 45533-45533

  • DOI: 10.1038/srep45533
  • Primary Citation of Related Structures:  
    5LGK

  • PubMed Abstract: 
  • The antibody IgE plays a central role in allergic disease mechanisms. Its effector functions are controlled through interactions between the Fc region and two principal cell surface receptors FcεRI and CD23. The interaction with FcεRI is primarily re ...

    The antibody IgE plays a central role in allergic disease mechanisms. Its effector functions are controlled through interactions between the Fc region and two principal cell surface receptors FcεRI and CD23. The interaction with FcεRI is primarily responsible for allergic sensitization and the inflammatory response, while IgE binding to CD23 is involved in the regulation of IgE synthesis and allergen transcytosis. Here we present the crystal structure of a CD23/IgE-Fc complex and conduct isothermal titration calorimetric binding studies. Two lectin-like "head" domains of CD23 bind to IgE-Fc with affinities that differ by more than an order of magnitude, but the crystal structure reveals only one head bound to one of the two identical heavy-chains in the asymmetrically bent IgE-Fc. These results highlight the subtle interplay between receptor binding sites in IgE-Fc and their affinities, the understanding of which may be exploited for therapeutic intervention in allergic disease.


    Organizational Affiliation

    Medical Research Council and Asthma UK Centre in Allergic Mechanisms of Asthma, London, U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ig epsilon chain C regionABCD307Homo sapiensMutation(s): 0 
Gene Names: IGHE
Find proteins for P01854 (Homo sapiens)
Explore P01854 
Go to UniProtKB:  P01854
NIH Common Fund Data Resources
PHAROS  P01854
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Low affinity immunoglobulin epsilon Fc receptorEF120Homo sapiensMutation(s): 0 
Gene Names: FCER2CD23ACLEC4JFCE2IGEBF
Find proteins for P06734 (Homo sapiens)
Explore P06734 
Go to UniProtKB:  P06734
NIH Common Fund Data Resources
PHAROS  P06734
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H
3 N-Glycosylation
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, C
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.267 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.52α = 117.87
b = 85.32β = 90.32
c = 88.23γ = 112.62
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United Kingdom--
Wellcome TrustUnited Kingdom--
Asthma UKUnited Kingdom--

Revision History 

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-04-12
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Advisory, Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary