PDB-9nph: X-ray crystal structure of recombinant Can f 1 in complex with hu...

ID or keywords:

Entry

Database: PDB / ID: 9nph

Title

X-ray crystal structure of recombinant Can f 1 in complex with human IgE mAb 1J11 Fab

Components

1J11 Fab heavy chain
1J11 Fab light chain
Major allergen Can f 1

Keywords

ALLERGEN/IMMUNE SYSTEM / allergen-antibody complex / dog allergen Can f 1 / anti Can f 1 antibody / human IgE bound to Can f 1 / ALLERGEN-IMMUNE SYSTEM complex / ALLERGEN

Function / homology

von Ebner's gland protein/ Bos/Can allergen / Lipocalin / small molecule binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / extracellular space / Major allergen Can f 1

Function and homology information

Biological species

Homo sapiens (human)

Canis lupus familiaris (dog)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.592 Å

Authors

Khatri, K. / Ball, A. / Smith, S.A. / Champan, M.D. / Pomes, A. / Chruszcz, M.

Funding support

United States, 1items

Citation

Journal: Protein Sci. / Year: 2025
Title: Human IgE monoclonal antibodies define two unusual epitopes trapping dog allergen Can f 1 in different conformations.
Authors: Khatri, K. / Ball, A. / Glesner, J. / Linn, C. / Vailes, L.D. / Wunschmann, S. / Gabel, S.A. / Zhang, J. / Peebles Jr., R.S. / Borowski, T. / Mueller, G.A. / Chapman, M.D. / Smith, S.A. / ...

History

Deposition	Mar 11, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 27, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9nph.cif.gz	307.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9nph.ent.gz	192.1 KB	Display	PDB format
PDBx/mmJSON format	9nph.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9nph_validation.pdf.gz	746.2 KB	Display	wwPDB validaton report
Full document	9nph_full_validation.pdf.gz	755.3 KB	Display
Data in XML	9nph_validation.xml.gz	27.5 KB	Display
Data in CIF	9nph_validation.cif.gz	36.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/np/9nph ftp://data.pdbj.org/pub/pdb/validation_reports/np/9nph	HTTPS FTP

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Related structure data

Related structure data	9npgC 9npiC 8vqf 8vqg 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	#193 - Jan 2016 Siderocalin similarity (5) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #78 - Jun 2006 Luciferase similarity (1)

Deposited unit

A: 1J11 Fab light chain

B: 1J11 Fab heavy chain

C: Major allergen Can f 1

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	69.511, 69.511, 247.040
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

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Antibody , 2 types, 2 molecules AB

#1: Antibody	1J11 Fab light chain Mass: 22717.029 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)
#2: Antibody	1J11 Fab heavy chain Mass: 25320.529 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

#3: Protein

Major allergen Can f 1 / Allergen Dog 1

Mass: 16569.699 Da / Num. of mol.: 1 / Mutation: C118S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Canis lupus familiaris (dog) / Production host:

Escherichia coli (E. coli) / References: UniProt: O18873

#4: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₅NO₆ / Feature type: SUBJECT OF INVESTIGATION

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 3 types, 75 molecules

#5: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#6: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO₄
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
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: 2.67 Å³/Da / Density % sol: 53 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Lithium sulfate monohydrate, 0.1 M HEPES , 25% w/v PEG 3,350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.979 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 25, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.59→40 Å / Num. obs: 20567 / % possible obs: 91.6 % / Redundancy: 9.9 % / CC_1/2: 0.979 / CC star: 0.995 / R_merge(I) obs: 0.122 / R_pim(I) all: 0.037 / R_rim(I) all: 0.128 / Net I/σ(I): 15.9
Reflection shell	Resolution: 2.59→2.63 Å / Redundancy: 9.6 % / R_merge(I) obs: 0.66 / Num. unique obs: 1008 / CC_1/2: 0.995 / CC star: 0.962 / R_pim(I) all: 0.192 / R_rim(I) all: 0.691 / % possible all: 93.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.592→38.221 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.904 / SU B: 27.721 / SU ML: 0.282 / Cross valid method: FREE R-VALUE / ESU R: 1.082 / ESU R Free: 0.342
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.261	1013	4.94 %
R_work	0.2153	19494	-
all	0.218	-	-
obs	-	20507	91.459 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 56.963 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.172 Å²	0.086 Å²	-0 Å²
2-	-	0.172 Å²	-0 Å²
3-	-	-	-0.559 Å²

Refinement step

Cycle: LAST / Resolution: 2.592→38.221 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4373	0	109	60	4542

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	4570
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	4082
X-RAY DIFFRACTION	r_angle_refined_deg	1.506	1.804	6246
X-RAY DIFFRACTION	r_angle_other_deg	0.953	1.728	9435
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.577	5	586
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.866	5	16
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.556	10	670
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	12.236	10	173
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	723
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	5310
X-RAY DIFFRACTION	r_gen_planes_other	0.013	0.02	978
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.2	764
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.235	0.2	3837
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	2173
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.094	0.2	2309
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.303	0.2	142
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.011	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.222	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.378	0.2	87
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.088	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	3.532	3.659	2353
X-RAY DIFFRACTION	r_mcbond_other	3.532	3.659	2353
X-RAY DIFFRACTION	r_mcangle_it	5.708	6.568	2936
X-RAY DIFFRACTION	r_mcangle_other	5.707	6.568	2937
X-RAY DIFFRACTION	r_scbond_it	4.542	3.959	2217
X-RAY DIFFRACTION	r_scbond_other	4.212	3.794	2166
X-RAY DIFFRACTION	r_scangle_it	6.907	7.161	3310
X-RAY DIFFRACTION	r_scangle_other	6.473	6.882	3233
X-RAY DIFFRACTION	r_lrange_it	10.22	42.749	18011
X-RAY DIFFRACTION	r_lrange_other	10.182	42.72	17995

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
2.592-2.659	0.355	72	0.293	1399	0.296	1605	0.906	0.942	91.6511	0.273
2.659-2.731	0.303	81	0.296	1360	0.297	1562	0.925	0.941	92.2535	0.275
2.731-2.81	0.37	55	0.295	1343	0.297	1523	0.923	0.942	91.7925	0.267
2.81-2.896	0.364	53	0.258	1333	0.262	1520	0.916	0.955	91.1842	0.229
2.896-2.991	0.356	61	0.253	1299	0.257	1425	0.929	0.956	95.4386	0.227
2.991-3.095	0.279	71	0.243	1206	0.245	1396	0.944	0.959	91.4756	0.22
3.095-3.211	0.285	63	0.245	1197	0.247	1372	0.944	0.959	91.8367	0.221
3.211-3.341	0.243	71	0.23	1140	0.231	1327	0.953	0.966	91.2585	0.212
3.341-3.488	0.334	35	0.23	1115	0.233	1254	0.936	0.97	91.7065	0.213
3.488-3.657	0.283	49	0.226	1060	0.228	1218	0.953	0.97	91.0509	0.207
3.657-3.853	0.255	62	0.22	999	0.223	1152	0.961	0.971	92.1007	0.202
3.853-4.084	0.3	35	0.2	956	0.203	1096	0.941	0.974	90.4197	0.188
4.084-4.363	0.278	44	0.167	899	0.172	1035	0.952	0.982	91.1111	0.155
4.363-4.707	0.185	56	0.144	836	0.147	965	0.98	0.987	92.4352	0.138
4.707-5.148	0.227	49	0.158	784	0.162	902	0.97	0.983	92.3503	0.15
5.148-5.743	0.242	55	0.182	689	0.186	831	0.964	0.979	89.5307	0.169
5.743-6.607	0.216	37	0.201	629	0.202	732	0.978	0.977	90.9836	0.187
6.607-8.032	0.149	19	0.211	543	0.209	640	0.989	0.971	87.8125	0.202
8.032-11.116	0.24	35	0.192	426	0.195	515	0.966	0.977	89.5146	0.203
11.116-38.221	0.275	10	0.303	281	0.302	341	0.96	0.951	85.3372	0.33

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	1.5246	-0.993	0.0695	1.4562	0.0449	2.1068	0.1061	0.2031	0.0635	0.041	-0.0234	-0.162	-0.0378	0.1665	-0.0827	0.1703	0.157	0.0214	0.3703	0	0.0311	3.892	-6.759	-16.885
2	0.7919	1.1704	0.1279	2.4278	1.4335	2.2873	-0.2286	0.0307	0.1604	-0.3528	0.1509	0.2502	-0.1496	0.058	0.0777	0.2925	0.23	-0.1151	0.3915	-0.0661	0.0534	-6.785	-19.623	-35.205
3	2.0952	-0.3702	0.5664	2.1345	1.0134	1.0519	0.1607	0.1883	-0.0422	-0.2114	-0.1723	0.1606	-0.1157	-0.1502	0.0115	0.1465	0.2036	-0.0255	0.3443	-0.013	0.0286	-17.617	0.476	-15.189
4	3.5474	-0.0622	-0.1927	0.8748	0.2796	0.964	-0.4063	-0.3105	-0.0092	0.089	-0.0748	0.0727	0.1885	-0.4059	0.4811	0.3208	0.0428	0.0476	0.4354	-0.1791	0.2596	-19.321	-34.168	-39.772
5	2.1615	-1.1424	-0.4825	2.575	0.8924	0.925	0.1582	0.0062	0.4331	-0.077	-0.0391	-0.2478	-0.1328	-0.0838	-0.1191	0.1679	0.163	0.0263	0.1959	0.0408	0.1754	-5.86	25.815	-8.165
6	2.8563	1.3755	-0.0158	3.0589	0.3916	3.7893	0.0231	-0.1862	0.4909	0.0423	0.0426	-0.1284	-0.4901	0.1175	-0.0656	0.1658	0.122	0.0279	0.2034	-0.0137	0.1481	-0.284	29.208	-2.653

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	2 - 79
2	X-RAY DIFFRACTION	2	ALL	A	80 - 208

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