6Y0M

Crystal structure of human CD23 lectin domain N225D, K229E, S252N, T251N mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 2.3 of the entry. See complete history


Literature

Reviving lost binding sites: Exploring calcium-binding site transitions between human and murine CD23.

Ilkow, V.F.Davies, A.M.Dhaliwal, B.Beavil, A.J.Sutton, B.J.McDonnell, J.M.

(2021) FEBS Open Bio 11: 1827-1840

  • DOI: https://doi.org/10.1002/2211-5463.13214
  • Primary Citation of Related Structures:  
    6Y0L, 6Y0M

  • PubMed Abstract: 

    Immunoglobulin E (IgE) is a central regulatory and triggering molecule of allergic immune responses. IgE's interaction with CD23 modulates both IgE production and functional activities.CD23 is a noncanonical immunoglobulin receptor, unrelated to receptors of other antibody isotypes. Human CD23 is a calcium-dependent (C-type) lectin-like domain that has apparently lost its carbohydrate-binding capability. The calcium-binding site classically required for carbohydrate binding in C-type lectins is absent in human CD23 but is present in the murine molecule. To determine whether the absence of this calcium-binding site affects the structure and function of human CD23, CD23 mutant proteins with increasingly "murine-like" sequences were generated. Restoration of the calcium-binding site was confirmed by NMR spectroscopy, and structures of mutant human CD23 proteins were determined by X-ray crystallography, although no electron density for calcium was observed. This study offers insights into the evolutionary differences between murine and human CD23 and some of the functional differences between CD23 in different species.


  • Organizational Affiliation

    Randall Centre for Cell & Molecular Biophysics, King's College London, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Low affinity immunoglobulin epsilon Fc receptor membrane-bound form143Homo sapiensMutation(s): 4 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 
  • Space Group: P 6 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.186α = 90
b = 115.186β = 90
c = 45.752γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomG1100090
Wellcome TrustUnited Kingdom085944

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-16
    Type: Initial release
  • Version 2.0: 2021-06-23
    Changes: Advisory, Atomic model, Database references, Derived calculations, Experimental preparation, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2021-07-07
    Changes: Database references
  • Version 2.2: 2021-07-14
    Changes: Database references
  • Version 2.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description