9Y0A | pdb_00009y0a

Crystal structure of Bet v 1.0101 in complex with human IgE Fab 2H22

• PDB DOI: https://doi.org/10.2210/pdb9Y0A/pdb

• Classification: ALLERGEN/IMMUNE SYSTEM
• Organism(s): Betula pendula, Homo sapiens
• Expression System: Escherichia coli, 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: 2.12 Å
• R-Value Free: 
  0.218 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.184 (DCC) 

Starting Models: in silico, 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 81: 2201-2203

• PubMed: 41622586 
• DOI: https://doi.org/10.1111/all.70240
• Primary Citation 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 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 65.34 kDa 
• Atom Count: 4,927 
• Modeled Residue Count: 598 
• Deposited Residue Count: 603 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major pollen allergen Bet v 1-A	A [auth C]	160	Betula pendula	Mutation(s): 0  Gene Names: BETVIA, BETVI
UniProt
Find proteins for P15494 (Betula pendula) Explore P15494  Go to UniProtKB:  P15494

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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
hIgE Fab 2H22 light chain	C [auth B]	216	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G79924RM GlyCosmos: G79924RM GlyGen: G79924RM

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	F [auth C], H [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	E [auth C], G [auth A], I [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL	J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free:  0.218 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.184 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.928	α = 90
b = 117.535	β = 90
c = 158.622	γ = 90

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
  
• Version 1.1: 2026-06-24
  Changes: Database references