2XA8 | pdb_00002xa8

Crystal structure of the Fab domain of omalizumab at 2.41A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 
    0.269 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Structural and Physical Basis for Anti-IgE Therapy.

Wright, J.D.Chu, H.M.Huang, C.H.Ma, C.Chang, T.W.Lim, C.

(2015) Sci Rep 5: 11581-11581

  • DOI: https://doi.org/10.1038/srep11581
  • Primary Citation Related Structures: 
    2XA8

  • PubMed Abstract: 

    Omalizumab, an anti-IgE antibody, used to treat severe allergic asthma and chronic idiopathic urticaria, binds to IgE in blood or membrane-bound on B lymphocytes but not to IgE bound to its high (FcεRI) or low (CD23) affinity receptor. Mutagenesis studies indicate overlapping FcεRI and omalizumab-binding sites in the Cε3 domain, but crystallographic studies show FcεRI and CD23-binding sites that are far apart, so how can omalizumab block IgE from binding both receptors? We report a 2.42-Å omalizumab-Fab structure, a docked IgE-Fc/omalizumab-Fab structure consistent with available experimental data, and the free energy contributions of IgE residues to binding omalizumab, CD23, and FcεRI. These results provide a structural and physical basis as to why omalizumab cannot bind receptor-bound IgE and why omalizumab-bound IgE cannot bind to CD23/FcεRI. They reveal the key IgE residues and their roles in binding omalizumab, CD23, and FcεRI.


  • Organizational Affiliation
    • 1] Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan [2] The Genomics Research Center, Academia Sinica 115, Taiwan.

Macromolecule Content 

  • Total Structure Weight: 47.22 kDa 
  • Atom Count: 3,397 
  • Modeled Residue Count: 437 
  • Deposited Residue Count: 437 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
OMALIZUMAB HEAVY CHAINA [auth H]219Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
OMALIZUMAB LIGHT CHAINB [auth L]218Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free:  0.269 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.6α = 90
b = 73.851β = 90
c = 141.126γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-11
    Type: Initial release
  • Version 1.1: 2016-01-27
    Changes: Database references, Version format compliance
  • Version 1.2: 2019-09-18
    Changes: Data collection, Database references, Experimental preparation
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Other, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary