4J4P | pdb_00004j4p

The complex of human IgE-Fc with two bound Fab fragments


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 
    0.284 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.236 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 
    0.239 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4J4P

This is version 2.1 of the entry. See complete history

Literature

Human immunoglobulin E flexes between acutely bent and extended conformations.

Drinkwater, N.Cossins, B.P.Keeble, A.H.Wright, M.Cain, K.Hailu, H.Oxbrow, A.Delgado, J.Shuttleworth, L.K.Kao, M.W.McDonnell, J.M.Beavil, A.J.Henry, A.J.Sutton, B.J.

(2014) Nat Struct Mol Biol 21: 397-404

  • DOI: https://doi.org/10.1038/nsmb.2795
  • Primary Citation Related Structures: 
    4J4P

  • PubMed Abstract: 

    Crystallographic and solution studies have shown that IgE molecules are acutely bent in their Fc region. Crystal structures reveal the Cɛ2 domain pair folded back onto the Cɛ3-Cɛ4 domains, but is the molecule exclusively bent or can the Cɛ2 domains adopt extended conformations and even 'flip' from one side of the molecule to the other? We report the crystal structure of IgE-Fc captured in a fully extended, symmetrical conformation and show by molecular dynamics, calorimetry, stopped-flow kinetic, surface plasmon resonance (SPR) and Förster resonance energy transfer (FRET) analyses that the antibody can indeed adopt such extended conformations in solution. This diversity of conformational states available to IgE-Fc offers a new perspective on IgE function in allergen recognition, as part of the B-cell receptor and as a therapeutic target in allergic disease.


  • Organizational Affiliation
    • King's College London, Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, London, SE1 1UL, UK.

Macromolecule Content 

  • Total Structure Weight: 177.75 kDa 
  • Atom Count: 11,702 
  • Modeled Residue Count: 1,508 
  • Deposited Residue Count: 1,614 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ig epsilon chain C region
A, B
323Homo sapiensMutation(s): 2 
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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01854-2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Immunoglobulin G Fab Fragment Heavy ChainC [auth H],
E [auth C]
249Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Immunoglobulin G Fab Fragment Light ChainD [auth L],
F [auth D]
235Homo sapiensMutation(s): 0 

Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-3)-[beta-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 E],
H [auth F]
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G89225LT
GlyCosmos: G89225LT
GlyGen: G89225LT

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free:  0.284 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.236 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 0.239 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.59α = 90
b = 100.81β = 90
c = 219.68γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2014-04-16
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2024-11-06
    Changes: Advisory, Data collection, Database references, Structure summary