Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - B2 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - C2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - B2 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - C2 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 301.11 kDa 
• Atom Count: 20626 
• Modelled Residue Count: 2604 
• Deposited Residue Count: 2680 
• Unique protein chains: 3

5HYS

Structure of IgE complexed with omalizumab

• PDB DOI: 10.2210/pdb5HYS/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus, Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2016-02-01 Released: 2016-06-01 
• Deposition Author(s): Pennington, L.F., Tarchevskaya, S.S., Sathiyamoorthy, K., Jardetzky, T.S.
• Funding Organization(s): Department of Defense (DOD, United States), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

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 

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

• PubMed: 27194387 
• 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. 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epididymis luminal protein 214	C [auth A], E [auth C], G [auth E], A [auth H]	222	Homo sapiens	Mutation(s): 0  Gene Names: HEL-214

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	D [auth B], F [auth D], H [auth F], B [auth L]	218	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ig epsilon chain C region	I [auth G], J [auth I], K [auth J], L [auth K]	230	Homo sapiens	Mutation(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

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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-glucopyranose	M, N, O, P	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	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

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 = 100.103	α = 90
b = 107.143	β = 95.18
c = 151.043	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
PHENIX	phasing
HKL-2000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-02-01 
• Released Date: 2016-06-01 
Deposition Author(s): Pennington, L.F., Tarchevskaya, S.S., Sathiyamoorthy, K., Jardetzky, T.S.

---

Funding Organization	Location	Grant Number
Department of Defense (DOD, United States)	United States	PR130130
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19 AI104209
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	T32 AI007290

Revision History  

• 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