9Y0D | pdb_00009y0d

Crystal structure of human IgE Fab 2H22

• PDB DOI: https://doi.org/10.2210/pdb9Y0D/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2025-08-28 Released: 2026-02-11 
• Deposition Author(s): O'Malley, A., Borders, B.T., Smith, S.A., Chruszcz, M.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.243 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.197 (DCC) 

Starting Model: experimental

Literature

Structural Determination of a Human IgE Epitope on Major Birch Allergen Bet v 1.

O'Malley, A., Borders, B.T., Wilson, J.M., Smith, S.A., Chruszcz, M.

(2026) Allergy 

• PubMed: 41622586 
• DOI: https://doi.org/10.1111/all.70240
• Primary Citation of Related Structures:  
  9Y0A, 9Y0D, 9Y0E

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA.
Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.
Division of Asthma, Allergy, and Clinical Immunology, University of Virginia School of Medicine, Charlottesville, Virginia, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 47.12 kDa 
• Atom Count: 3,422 
• Modeled Residue Count: 437 
• Deposited Residue Count: 443 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hIgE Fab 2H22 heavy chain	A	227	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
hIgE Fab 2H22 light chain	B	216	Homo sapiens	Mutation(s): 0
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PEG	C [auth A], D [auth B], F [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.243 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.197 (DCC) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.769	α = 90
b = 116.769	β = 90
c = 71.102	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-11 
Deposition Author(s): O'Malley, A., Borders, B.T., Smith, S.A., Chruszcz, M.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2026-02-11
  Type: Initial release