3H9Y

Crystal structure of the IgE-Fc3-4 domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Conformational flexibility in immunoglobulin E-Fc 3-4 revealed in multiple crystal forms.

Wurzburg, B.A.Jardetzky, T.S.

(2009) J.Mol.Biol. 393: 176-190

  • DOI: 10.1016/j.jmb.2009.08.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structure of immunoglobulin E (IgE)-Fc(3-4) has been solved in three new crystal forms, providing 13 snapshots of the Fc conformation and revealing a diverse range of open-closed motions among subunit chains and dimers. A more detailed analysis o ...

    The structure of immunoglobulin E (IgE)-Fc(3-4) has been solved in three new crystal forms, providing 13 snapshots of the Fc conformation and revealing a diverse range of open-closed motions among subunit chains and dimers. A more detailed analysis of the open-to-closed motion of IgE-Fc(3-4) was possible with so many structures, and the new structures allow a more thorough examination of the flexibility of IgE-Fc and its implications for receptor binding. The existence of a hydrophobic pocket at the elbow region of the Fc appears to be conformation dependent and suggests a means of regulating the IgE-Fc conformation (and potentially receptor binding) with small molecules.


    Organizational Affiliation

    Department of Structural Biology, Stanford University, Stanford, CA 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ig epsilon chain C region
A, B, E
223Homo sapiensMutation(s): 2 
Gene Names: IGHE
Find proteins for P01854 (Homo sapiens)
Go to UniProtKB:  P01854
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B, E
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B, E
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NH4
Query on NH4

Download SDF File 
Download CCD File 
E
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.231 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 153.676α = 90.00
b = 104.994β = 101.61
c = 49.222γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-04-30 
  • Released Date: 2009-09-08 
  • Deposition Author(s): Wurzburg, B.A.

Revision History 

  • Version 1.0: 2009-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description
  • Version 1.3: 2018-05-30
    Type: Data collection, Derived calculations