PDB-9y0a: Crystal structure of Bet v 1.0101 in complex with human IgE Fab 2H22

ID or keywords:

Entry

Database: PDB / ID: 9y0a

Title

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

Components

(hIgE Fab 2H22 ...) x 2
Major pollen allergen Bet v 1-A

Keywords

ALLERGEN/IMMUNE SYSTEM / allergen / human IgE / IgE Fab / allergen-antibody complex / ALLERGEN-IMMUNE SYSTEM complex

Function / homology

Function and homology information

abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / nucleus / cytoplasm
Similarity search - Function

Biological species

Betula pendula (European white birch)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.12 Å

Authors

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

Funding support

United States, 1items

Citation

Journal: Allergy / Year: 2026
Title: Structural Determination of a Human IgE Epitope on Major Birch Allergen Bet v 1.
Authors: O'Malley, A. / Borders, B.T. / Wilson, J.M. / Smith, S.A. / Chruszcz, M.

History

Deposition	Aug 28, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 11, 2026	Provider: repository / Type: Initial release
Revision 1.1	Jun 24, 2026	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9y0a.cif.gz	319.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9y0a.ent.gz	199.9 KB	Display	PDB format
PDBx/mmJSON format	9y0a.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y0/9y0a ftp://data.pdbj.org/pub/pdb/validation_reports/y0/9y0a	HTTPS FTP

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Related structure data

Related structure data	9y0dC 9y0eC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

C: Major pollen allergen Bet v 1-A

A: hIgE Fab 2H22 heavy chain

B: hIgE Fab 2H22 light chain

hetero molecules

65.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	81.928, 117.535, 158.622
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

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Antibody , 2 types, 2 molecules AB

#2: Antibody	hIgE Fab 2H22 heavy chain Mass: 23953.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody	hIgE Fab 2H22 light chain Mass: 22630.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Protein / Sugars , 2 types, 2 molecules C

#1: Protein

Major pollen allergen Bet v 1-A / Allergen Bet v I-A

Mass: 17592.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Betula pendula (European white birch) / Gene: BETVIA, BETVI / Production host:

Escherichia coli (E. coli) / References: UniProt: P15494

#4: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-3DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a3-b1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{}}	LINUCS	PDB-CARE

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Non-polymers , 4 types, 378 molecules

#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#7: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.98 Å³/Da / Density % sol: 57 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5; 0.05 M magnesium chloride hexahydrate; 30% PEG MME 550

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 11, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.873 Å / Relative weight: 1
Reflection	Resolution: 2.12→40 Å / Num. obs: 43908 / % possible obs: 99.8 % / Redundancy: 12.6 % / CC_1/2: 0.998 / CC star: 1 / R_merge(I) obs: 0.087 / R_pim(I) all: 0.026 / R_rim(I) all: 0.091 / Net I/σ(I): 25.5
Reflection shell	Resolution: 2.12→2.16 Å / Redundancy: 11.1 % / R_merge(I) obs: 0.73 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2152 / CC_1/2: 0.866 / CC star: 0.963 / R_pim(I) all: 0.224 / R_rim(I) all: 0.764 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
HKL-3000		data reduction
HKL-3000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.12→39.694 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.948 / SU B: 9.781 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.162
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2183	2224	5.091 %	RANDOM
R_work	0.1708	41459	-	-
all	0.173	-	-	-
obs	-	43683	99.783 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 59.23 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.789 Å²	0 Å²	-0 Å²
2-	-	-0.775 Å²	0 Å²
3-	-	-	-1.015 Å²

Refinement step

Cycle: LAST / Resolution: 2.12→39.694 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4457	0	76	372	4905

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	4664
X-RAY DIFFRACTION	r_bond_other_d	0.011	0.016	4303
X-RAY DIFFRACTION	r_angle_refined_deg	1.573	1.798	6350
X-RAY DIFFRACTION	r_angle_other_deg	0.822	1.726	9987
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.98	5	600
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.879	5	12
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.323	10	704
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	12.693	10	168
X-RAY DIFFRACTION	r_chiral_restr	0.128	0.2	720
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	5392
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	988
X-RAY DIFFRACTION	r_nbd_refined	0.197	0.2	701
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.212	0.2	3737
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.2	2222
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.092	0.2	2270
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.195	0.2	295
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.083	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.126	0.2	22
X-RAY DIFFRACTION	r_nbd_other	0.203	0.2	69
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.189	0.2	14
X-RAY DIFFRACTION	r_mcbond_it	3.677	4.412	2397
X-RAY DIFFRACTION	r_mcbond_other	3.676	4.412	2397
X-RAY DIFFRACTION	r_mcangle_it	4.767	7.915	2992
X-RAY DIFFRACTION	r_mcangle_other	4.767	7.916	2993
X-RAY DIFFRACTION	r_scbond_it	5.226	4.937	2267
X-RAY DIFFRACTION	r_scbond_other	5.225	4.94	2268
X-RAY DIFFRACTION	r_scangle_it	7.222	8.818	3356
X-RAY DIFFRACTION	r_scangle_other	7.221	8.82	3357
X-RAY DIFFRACTION	r_lrange_it	9.939	55.5	19053
X-RAY DIFFRACTION	r_lrange_other	9.948	55.075	18819

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.12-2.175	0.318	158	0.259	3041	0.262	3206	0.94	0.958	99.7817	0.243
2.175-2.234	0.252	168	0.23	2937	0.232	3113	0.957	0.966	99.743	0.208
2.234-2.299	0.308	146	0.246	2838	0.249	2995	0.935	0.958	99.6327	0.227
2.299-2.369	0.237	153	0.191	2773	0.194	2935	0.96	0.976	99.6934	0.174
2.369-2.447	0.243	145	0.172	2723	0.176	2873	0.963	0.982	99.826	0.152
2.447-2.532	0.242	145	0.183	2584	0.187	2733	0.962	0.978	99.8536	0.163
2.532-2.628	0.243	139	0.178	2554	0.181	2697	0.959	0.98	99.8517	0.156
2.628-2.734	0.21	112	0.172	2473	0.174	2589	0.972	0.982	99.8455	0.149
2.734-2.855	0.233	126	0.176	2324	0.179	2455	0.967	0.981	99.7963	0.154
2.855-2.994	0.215	112	0.181	2252	0.182	2368	0.968	0.98	99.8311	0.16
2.994-3.155	0.218	108	0.179	2145	0.181	2256	0.968	0.98	99.867	0.164
3.155-3.345	0.259	100	0.185	2031	0.188	2134	0.959	0.979	99.8594	0.173
3.345-3.574	0.227	107	0.186	1923	0.188	2031	0.968	0.979	99.9508	0.176
3.574-3.858	0.227	103	0.165	1762	0.169	1865	0.968	0.983	100	0.158
3.858-4.222	0.198	97	0.145	1650	0.148	1755	0.98	0.987	99.5442	0.142
4.222-4.714	0.155	83	0.127	1498	0.129	1582	0.987	0.991	99.9368	0.129
4.714-5.43	0.188	63	0.138	1346	0.14	1409	0.98	0.99	100	0.14
5.43-6.62	0.18	68	0.154	1136	0.156	1204	0.981	0.986	100	0.157
6.62-9.234	0.263	49	0.165	914	0.17	963	0.959	0.983	100	0.175
9.234-39.694	0.196	41	0.18	544	0.181	592	0.982	0.981	98.8176	0.192

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.7095	-0.8123	-1.9534	2.5228	-1.9562	4.3222	-0.2345	-0.1695	0.4471	0.6232	0.3211	-0.2679	-0.5009	-0.0958	-0.0866	0.2104	0.0185	-0.1171	0.3676	-0.0122	0.1932	12.488	46.819	23.501
2	0.5973	-0.0743	0.3148	2.3228	-2.0854	2.3907	-0.1358	-0.0721	0.0811	0.2646	-0.0207	-0.2857	-0.2502	0.0357	0.1565	0.065	0.0193	-0.0587	0.3208	-0.0264	0.0863	17.842	40.049	25.863
3	8.5292	2.7777	1.0663	1.7185	1.4898	2.4978	0.0328	0.39	-0.3101	0.1371	0.0807	-0.0589	0.0018	-0.2218	-0.1135	0.1196	-0.0223	0.0093	0.3244	0.0068	0.0615	-9.002	48.071	-0.036
4	2.1183	-0.132	-0.4283	0.8979	0.2253	1.9843	-0.0315	0.0326	-0.0447	0.1535	0.0765	-0.0102	-0.0078	-0.2392	-0.045	0.104	-0.0034	0.025	0.3343	0.0179	0.0218	-6.908	46.297	6.467
5	1.2517	0.0739	0.7868	0.7941	0.0399	0.8818	-0.0505	-0.0903	-0.0369	-0.0806	0.0276	-0.055	0.152	0.0047	0.0228	0.0982	0.0153	0.0186	0.3476	0.0111	0.0653	10.802	20.561	25.037
6	0.4262	-0.4529	0.6095	0.6901	-0.7441	1.5004	0.0492	-0.0688	-0.0146	-0.1943	0.0514	-0.0018	0.141	-0.1132	-0.1006	0.1077	-0.0411	0.0098	0.3448	-0.0009	0.0465	-1.891	33.698	2.835
7	0.731	-0.2432	1.2999	1.3235	-0.9714	2.6626	0.0021	0.0558	-0.0704	-0.1474	0.0827	-0.0606	0.1847	-0.039	-0.0848	0.1412	-0.0328	0.013	0.3529	-0.0309	0.0415	-4.423	35.569	-8.974
8	6.1331	-6.7934	4.5303	15.4543	-4.0904	3.5389	0.1279	-0.2828	-0.1911	-0.5475	0.0336	0.7653	0.1528	-0.3625	-0.1615	0.2263	-0.0751	-0.0818	0.5202	-0.0017	0.2317	-14.969	40.917	-11.478
9	2.291	-0.1343	1.3883	1.3082	1.3575	3.0319	0.0621	-0.1333	-0.095	-0.0106	0.1017	-0.0099	0.1194	-0.0632	-0.1638	0.0739	0.0533	0.0034	0.3476	0.0594	0.0252	17.784	21.292	47.095
10	4.7475	-0.304	1.5639	1.5896	-0.6557	0.7432	-0	-0.3665	-0.0827	0.3003	0.0184	-0.0299	-0.1674	-0.1688	-0.0184	0.2246	0.0367	-0.0475	0.4021	0.0086	0.0621	22.807	22.493	62.827
11	2.6078	-1.1992	2.9754	1.3603	-1.2211	3.5543	0.0222	0.1121	-0.1063	0.0637	0.035	-0.0384	-0.0455	0.0803	-0.0572	0.0881	0.0414	-0.0476	0.3666	0.0039	0.0733	24.328	21.58	49.846
12	7.0494	-3.746	-1.2073	2.6861	1.1966	1.5519	-0.076	0.096	-0.6825	0.2393	-0.009	0.3713	0.4247	-0.037	0.085	0.1513	0.0365	-0.0298	0.3075	-0.0034	0.1174	17.632	16.323	53.713

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	9	ALL	C	2 - 20
2	X-RAY DIFFRACTION	10	ALL	C	21 - 74
3	X-RAY DIFFRACTION	11	ALL	C	75 - 119
4	X-RAY DIFFRACTION	12	ALL	C	120 - 160

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