4J4P

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 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/nsmb.2795

  • 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 a ...

    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

    UCB Pharma, Slough, SL1 3WE, UK.,Medical Research Council & Asthma UK Centre in Allergic Mechanisms of Asthma, New Hunt's House, Guy's Campus, London, SE1 1UL, UK.,King's College London, Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, London, SE1 1UL, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ig epsilon chain C region
A, B
323Homo sapiensMutation(s): 2 
Gene Names: IGHE
Find proteins for P01854 (Homo sapiens)
Go to UniProtKB:  P01854
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Immunoglobulin G Fab Fragment Heavy Chain
H, C
249N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Immunoglobulin G Fab Fragment Light Chain
L, D
235N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 84.590α = 90.00
b = 100.810β = 90.00
c = 219.680γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
xia2data scaling
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2014-04-16
    Type: Database references