5HYS

Structure of IgE complexed with omalizumab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


This is version 2.0 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
  • Primary Citation of Related Structures:  
    5HYS

  • 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 both high- and low-affinity IgE receptors, and explains why omalizumab selectively binds free IgE ...

    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.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Epididymis luminal protein 214C [auth A],
E [auth C],
G [auth E],
A [auth H]
222Homo sapiensMutation(s): 0 
Gene Names: HEL-214
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinD [auth B],
F [auth D],
H [auth F],
B [auth L]
218Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ig epsilon chain C regionI [auth G],
J [auth I],
K [auth J],
L [auth K]
230Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01854
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseM, N, O, P 5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth A],
AB [auth I],
BA [auth B],
BB [auth I],
CA [auth B],
AA [auth A],
AB [auth I],
BA [auth B],
BB [auth I],
CA [auth B],
CB [auth I],
DA [auth B],
DB [auth J],
EA [auth B],
EB [auth J],
FA [auth C],
FB [auth J],
GA [auth C],
GB [auth J],
HA [auth C],
HB [auth K],
IA [auth C],
IB [auth K],
JA [auth D],
JB [auth K],
KA [auth D],
KB [auth K],
LA [auth D],
LB [auth K],
MA [auth D],
NA [auth D],
OA [auth D],
PA [auth E],
Q [auth H],
QA [auth E],
R [auth H],
RA [auth F],
S [auth H],
SA [auth F],
T [auth H],
TA [auth F],
U [auth L],
UA [auth F],
V [auth L],
VA [auth F],
W [auth L],
WA [auth G],
X [auth L],
XA [auth G],
Y [auth A],
YA [auth I],
Z [auth A],
ZA [auth I]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.103α = 90
b = 107.143β = 95.18
c = 151.043γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PHENIXphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2019-04-10
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary