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


This is version 2.1 of the entry. See complete history


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: https://doi.org/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 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

    Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ig epsilon chain C region
A, B, C, D
307Homo sapiensMutation(s): 0 
Gene Names: IGHE
UniProt & NIH Common Fund Data Resources
Find proteins for P01854 (Homo sapiens)
Explore P01854 
Go to UniProtKB:  P01854
PHAROS:  P01854
GTEx:  ENSG00000211891 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01854
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Low affinity immunoglobulin epsilon Fc receptor
E, F
120Homo sapiensMutation(s): 0 
Gene Names: FCER2CD23ACLEC4JFCE2IGEBF
UniProt & NIH Common Fund Data Resources
Find proteins for P06734 (Homo sapiens)
Explore P06734 
Go to UniProtKB:  P06734
PHAROS:  P06734
GTEx:  ENSG00000104921 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06734
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth A],
J [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
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

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • 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
  • Version 2.1: 2024-01-10
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary