PDB-8vqf: X-ray crystal structure of natural Can f 1 in complex with human ...

ID or keywords:

Entry

Database: PDB / ID: 8vqf

Title

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

Components

IgE 1J11 Heavy chain
IgE 1J11 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

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: 3.109 Å

Authors

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

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: X-ray crystal structure of natural Can f 1 in complex with human IgE 1J11 Fab
Authors: Khatri, K. / Ball, A. / Smith, S.A. / Champan, M.D. / Pomes, A. / Chruszcz, M.

History

Deposition	Jan 18, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 22, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8vqf.cif.gz	305.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8vqf.ent.gz	193.8 KB	Display	PDB format
PDBx/mmJSON format	8vqf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8vqf_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	8vqf_full_validation.pdf.gz	1.2 MB	Display
Data in XML	8vqf_validation.xml.gz	25.1 KB	Display
Data in CIF	8vqf_validation.cif.gz	32.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vq/8vqf ftp://data.pdbj.org/pub/pdb/validation_reports/vq/8vqf	HTTPS FTP

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Related structure data

Related structure data	8vqgC 7mlhS S: Starting model for refinement 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: IgE 1J11 Light chain

B: IgE 1J11 Heavy chain

C: Major allergen Can f 1

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: surface plasmon resonance

Unit cell

Length a, b, c (Å)	154.758, 154.758, 89.415
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	IgE 1J11 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	IgE 1J11 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, 3 molecules C

#3: Protein

Major allergen Can f 1 / Allergen Dog 1

Mass: 17340.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural)

Canis lupus familiaris (dog) / 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.: 2 / 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 , 2 types, 15 molecules

#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.73 Å³/Da / Density % sol: 73.98 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 2 M ammonium sulfate, 0.1 M Tris, pH 8 / PH range: 4.5-8

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 12, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.1→40 Å / Num. obs: 22392 / % possible obs: 99.9 % / Redundancy: 10 % / R_merge(I) obs: 0.16 / R_pim(I) all: 0.052 / R_rim(I) all: 0.168 / R_sym value: 0.16 / Net I/σ(I): 20.6
Reflection shell	Resolution: 3.1→3.15 Å / Redundancy: 11 % / R_merge(I) obs: 1.079 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1096 / CC_1/2: 0.89 / CC star: 0.97 / R_pim(I) all: 0.339 / R_rim(I) all: 1.132 / R_sym value: 1.079 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 7MLH

7mlh

Resolution: 3.109→39.964 Å / Cor.coef. F_o:F_c: 0.911 / Cor.coef. F_o:F_c free: 0.921 / WR_factor R_free: 0.245 / WR_factor R_work: 0.224 / SU B: 58.527 / SU ML: 0.407 / Average fsc free: 0.9385 / Average fsc work: 0.9443 / Cross valid method: FREE R-VALUE / ESU R: 0.877 / ESU R Free: 0.388
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2681	1166	5.211 %
R_work	0.2479	21211	-
all	0.249	-	-
obs	-	22377	99.347 %

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: 181.996 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.54 Å²	0.77 Å²	0 Å²
2-	-	1.54 Å²	-0 Å²
3-	-	-	-4.996 Å²

Refinement step

Cycle: LAST / Resolution: 3.109→39.964 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4324	0	88	3	4415

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	4504
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	4050
X-RAY DIFFRACTION	r_angle_refined_deg	0.938	1.806	6158
X-RAY DIFFRACTION	r_angle_other_deg	1.049	1.73	9357
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.086	5	576
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	2.43	5	17
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.581	10	671
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	11.908	10	171
X-RAY DIFFRACTION	r_chiral_restr	0.039	0.2	714
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	5251
X-RAY DIFFRACTION	r_gen_planes_other	0.012	0.02	971
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	813
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.219	0.2	3923
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	2196
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.095	0.2	2151
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.13	0.2	129
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.028	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.104	0.2	6
X-RAY DIFFRACTION	r_nbd_other	0.231	0.2	41
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.052	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	4.665	13.382	2316
X-RAY DIFFRACTION	r_mcbond_other	4.665	13.382	2316
X-RAY DIFFRACTION	r_mcangle_it	7.937	24.05	2888
X-RAY DIFFRACTION	r_mcangle_other	7.936	24.052	2889
X-RAY DIFFRACTION	r_scbond_it	7.133	14.398	2188
X-RAY DIFFRACTION	r_scbond_other	7.194	13.785	2141
X-RAY DIFFRACTION	r_scangle_it	11.425	26.294	3270
X-RAY DIFFRACTION	r_scangle_other	11.526	25.228	3199
X-RAY DIFFRACTION	r_lrange_it	18.763	127.086	4711
X-RAY DIFFRACTION	r_lrange_other	18.761	127.088	4712

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
3.109-3.189	0.433	75	0.43	1470	0.43	1661	0.874	0.853	93.0163	0.347
3.189-3.276	0.384	108	0.392	1467	0.391	1575	0.868	0.874	100	0.308
3.276-3.37	0.342	83	0.339	1459	0.339	1545	0.898	0.905	99.8058	0.277
3.37-3.473	0.343	66	0.306	1434	0.308	1500	0.909	0.929	100	0.244
3.473-3.586	0.271	83	0.277	1393	0.276	1476	0.947	0.947	100	0.219
3.586-3.711	0.279	64	0.272	1357	0.272	1422	0.949	0.949	99.9297	0.229
3.711-3.85	0.323	61	0.248	1295	0.251	1356	0.938	0.957	100	0.204
3.85-4.006	0.272	77	0.219	1227	0.222	1304	0.957	0.967	100	0.179
4.006-4.182	0.269	66	0.211	1244	0.214	1310	0.96	0.97	100	0.175
4.182-4.383	0.202	57	0.194	1133	0.194	1197	0.973	0.975	99.4152	0.167
4.383-4.617	0.171	55	0.169	1106	0.169	1161	0.982	0.983	100	0.143
4.617-4.893	0.218	59	0.182	1027	0.183	1086	0.968	0.98	100	0.161
4.893-5.226	0.262	61	0.205	984	0.208	1045	0.964	0.976	100	0.188
5.226-5.636	0.206	52	0.224	921	0.223	973	0.975	0.972	100	0.202
5.636-6.162	0.247	31	0.232	863	0.232	894	0.97	0.967	100	0.217
6.162-6.869	0.341	37	0.256	799	0.259	838	0.927	0.957	99.7613	0.243
6.869-7.893	0.341	37	0.247	674	0.251	711	0.935	0.961	100	0.248
7.893-9.574	0.225	34	0.235	590	0.234	624	0.984	0.973	100	0.249
9.574-13.167	0.257	46	0.235	461	0.237	507	0.971	0.98	100	0.241
13.167-39.964	0.273	14	0.42	306	0.412	324	0.98	0.906	98.7654	0.456

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	6.1454	1.3868	-0.5579	0.3364	0.0498	3.6343	0.0653	-0.4067	0.2122	0.014	-0.11	0.1092	0.264	0.2773	0.0447	0.9021	-0.1409	0.0766	0.3381	0.0357	0.3968	-83.4224	22.6422	21.3494
2	3.0126	-2.3241	-1.726	6.703	1.2131	1.171	0.2702	-0.0997	0.1329	0.6708	-0.2237	0.0332	0.3518	0.0748	-0.0465	1.7678	-0.0591	0.07	0.087	0.0011	0.0238	-92.0177	-7.0565	15.9446
3	1.9598	1.3715	-1.858	2.5653	0.086	3.4058	-0.3809	-0.2071	-0.0896	-0.3925	0.0567	0.1612	0.3916	0.84	0.3242	0.9174	0.0594	0.1543	0.5544	0.0535	0.3001	-68.5839	19.0553	6.0688
4	6.5325	3.3456	0.158	2.2468	1.5813	4.8808	0.0933	0.0829	-0.3622	0.0379	-0.1665	-0.0758	-0.8358	-0.4409	0.0732	1.3453	0.0659	0.1117	0.1908	-0.152	0.1634	-94.6982	-8.4835	-0.4173
5	4.3016	4.6775	-1.0894	5.092	-1.1749	0.3553	0.0654	-0.0426	0.3979	0.0435	0.0101	0.4112	0.0221	0.2448	-0.0755	0.4379	-0.341	0.1155	1.2039	0.0139	0.1976	-54.9861	43.0014	19.5259
6	10.786	1.4578	-3.8639	0.3404	0.0876	4.2243	-0.2521	-0.2381	-0.3785	0.0537	0.1412	-0.0004	0.6048	0.6643	0.1109	0.621	-0.087	0.0424	0.8219	-0.0084	0.3877	-52.1297	34.0867	18.9479
7	0.6948	1.2847	-0.5723	3.0958	0.9181	6.2082	0.0165	-0.0179	0.149	0.0035	0.0856	0.1813	-0.1024	0.3351	-0.1021	0.3297	-0.377	0.0067	0.8825	0.0819	0.3225	-54.0597	44.7288	23.5393
8	1.6806	0.3703	1.5837	7.4023	1.2676	4.5386	-0.2672	0.3063	0.4693	-0.2771	-0.1741	0.1158	-0.2721	0.7388	0.4413	0.3724	-0.3083	0.0242	0.9074	0.1676	0.2115	-47.1966	50.7313	16.2935

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	2 - 106
2	X-RAY DIFFRACTION	2	ALL	A	107 - 211

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