5HYS

Structure of IgE complexed with omalizumab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of omalizumab therapy and omalizumab-mediated IgE exchange.

Pennington, L.F.Tarchevskaya, S.Brigger, D.Sathiyamoorthy, K.Graham, M.T.Nadeau, K.C.Eggel, A.Jardetzky, T.S.

(2016) Nat Commun 7: 11610-11610

  • DOI: 10.1038/ncomms11610

  • PubMed Abstract: 
  • Omalizumab is a widely used therapeutic anti-IgE antibody. Here we report the crystal structure of the omalizumab-Fab in complex with an IgE-Fc fragment. This structure reveals the mechanism of omalizumab-mediated inhibition of IgE interactions with ...

    Omalizumab is a widely used therapeutic anti-IgE antibody. Here we report the crystal structure of the omalizumab-Fab in complex with an IgE-Fc fragment. This structure reveals the mechanism of omalizumab-mediated inhibition of IgE interactions with both high- and low-affinity IgE receptors, and explains why omalizumab selectively binds free IgE. The structure of the complex also provides mechanistic insight into a class of disruptive IgE inhibitors that accelerate the dissociation of the high-affinity IgE receptor from IgE. We use this structural data to generate a mutant IgE-Fc fragment that is resistant to omalizumab binding. Treatment with this omalizumab-resistant IgE-Fc fragment, in combination with omalizumab, promotes the exchange of cell-bound full-length IgE with omalizumab-resistant IgE-Fc fragments on human basophils. This combination treatment also blocks basophil activation more efficiently than either agent alone, providing a novel approach to probe regulatory mechanisms underlying IgE hypersensitivity with implications for therapeutic interventions.


    Organizational Affiliation

    Sean N. Parker Center for Allergy Research at Stanford University, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Rheumatology, Immunology and Allergology, University Hospital Bern, Bern 3012, Switzerland.,Progam in Immunology, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Clinical Research, University of Bern, Bern 3012, Switzerland.,Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Epididymis luminal protein 214
H, A, C, E
222N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
L, B, D, F
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ig epsilon chain C region
G, I, J, K
230Homo 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
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
G, I, J, K
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
G, I, J, K
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
G, I, J, K
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 100.103α = 90.00
b = 107.143β = 95.18
c = 151.043γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Defense (United States)United StatesPR130130
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesU19 AI104209
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesT32 AI007290

Revision History 

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Derived calculations
  • Version 1.2: 2019-04-10
    Type: Author supporting evidence, Data collection