PDB-7mlh: Crystal structure of human IgE (2F10) in complex with Der p 2.0103

ID or keywords:

Entry

Database: PDB / ID: 7mlh

Title

Crystal structure of human IgE (2F10) in complex with Der p 2.0103

Components

Der p 2 variant 3
IgE Heavy chain
IgE Light Chain

Keywords

ALLERGEN/IMMUNE SYSTEM / Allergy / IgE / House Dust Mites /

Antibody /

ALLERGEN / ALLERGEN-IMMUNE SYSTEM complex

Function / homology

Sterol transport protein NPC2-like /

ML domain / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / Immunoglobulin E-set / Der p 2 variant 3

Function and homology information

Biological species

Homo sapiens (human)

Dermatophagoides pteronyssinus (European house dust mite)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Khatri, K. / Kapingidza, A.B. / Richardson, C.M. / Vailes, L.D. / Wunschmann, S. / Dolamore, C. / Chapman, M.D. / Smith, S.A. / Pomes, A. / Chruszcz, M.

Funding support

United States, 1items

Citation

Journal: Pnas Nexus / Year: 2022
Title: Human IgE monoclonal antibody recognition of mite allergen Der p 2 defines structural basis of an epitope for IgE cross-linking and anaphylaxis in vivo.
Authors: Khatri, K. / Richardson, C.M. / Glesner, J. / Kapingidza, A.B. / Mueller, G.A. / Zhang, J. / Dolamore, C. / Vailes, L.D. / Wunschmann, S. / Peebles Jr., R.S. / Chapman, M.D. / Smith, S.A. / ...

History

Deposition	Apr 28, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 4, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 16, 2022	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7mlh.cif.gz	409.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7mlh.ent.gz	326.6 KB	Display	PDB format
PDBx/mmJSON format	7mlh.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/ml/7mlh ftp://data.pdbj.org/pub/pdb/validation_reports/ml/7mlh	HTTPS FTP

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Related structure data

Related structure data	1ktjS 6oy4S S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (2)

Deposited unit

A: IgE Light Chain

B: Der p 2 variant 3

C: IgE Heavy chain

D: IgE Light Chain

E: IgE Heavy chain

F: Der p 2 variant 3

hetero molecules

124 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: IgE Light Chain

C: IgE Heavy chain

F: Der p 2 variant 3

hetero molecules

defined by author&software
Evidence: native gel electrophoresis
61.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Der p 2 variant 3

D: IgE Light Chain

E: IgE Heavy chain

hetero molecules

defined by author&software
Evidence: native gel electrophoresis
62.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	51.776, 231.458, 51.791
Angle α, β, γ (deg.)	90.000, 94.338, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	D
3	2	B
4	2	F
5	3	C
6	3	E

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	ASP	ASP	PRO	PRO	A	A	1 - 208	1 - 208
2	2	1	ASP	ASP	PRO	PRO	D	D	1 - 208	1 - 208
3	1	2	ASP	ASP	ASP	ASP	B	B	1 - 129	1 - 129
4	2	2	ASP	ASP	ASP	ASP	F	F	1 - 129	1 - 129
5	1	3	GLN	GLN	PRO	PRO	C	C	1 - 219	1 - 219
6	2	3	GLN	GLN	PRO	PRO	E	E	1 - 219	1 - 219

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6

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Protein , 2 types, 4 molecules BFCE

#2: Protein	Der p 2 variant 3 Mass: 14141.363 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dermatophagoides pteronyssinus (European house dust mite) Production host: Komagataella pastoris (fungus) / References: UniProt: I2CMD6
#3: Protein	IgE Heavy chain Mass: 24133.943 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Antibody , 1 types, 2 molecules AD

#1: Antibody	IgE Light Chain Mass: 23015.592 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 3 types, 600 molecules

#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 582 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.52 Å³/Da / Density % sol: 51.27 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5 Details: Index A1, Salt: None; Buffer: 0.1M Citric acid pH 3.5; Precipitant: 2.0M Ammonium sulfate

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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: May 29, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.097→40 Å / Num. obs: 68319 / % possible obs: 96.6 % / Redundancy: 3.6 % / CC_1/2: 0.987 / CC star: 0.997 / R_merge(I) obs: 0.097 / R_pim(I) all: 0.058 / R_rim(I) all: 0.113 / R_sym value: 0.097 / Net I/σ(I): 16.9
Reflection shell	Resolution: 2.1→2.14 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.428 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3025 / CC_1/2: 0.824 / CC star: 0.95 / R_pim(I) all: 0.269 / R_rim(I) all: 0.509 / R_sym value: 0.428 / % possible all: 86.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1KTJ, 6OY4

1ktj

6oy4

Resolution: 2.1→38.606 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.924 / SU B: 12.512 / SU ML: 0.171 / Cross valid method: FREE R-VALUE / ESU R: 0.253 / ESU R Free: 0.198
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2466	3560	5.219 %
R_work	0.2104	64647	-
all	0.212	-	-
obs	-	68207	96.362 %

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: 42.213 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.086 Å²	0 Å²	-1.146 Å²
2-	-	-0.582 Å²	-0 Å²
3-	-	-	0.832 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→38.606 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8267	0	78	582	8927

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	8539
X-RAY DIFFRACTION	r_bond_other_d	0.036	0.017	7854
X-RAY DIFFRACTION	r_angle_refined_deg	1.54	1.644	11646
X-RAY DIFFRACTION	r_angle_other_deg	2.37	1.577	18194
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.009	5	1092
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.974	23.936	343
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.834	15	1351
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.995	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	1143
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	9642
X-RAY DIFFRACTION	r_gen_planes_other	0.009	0.02	1814
X-RAY DIFFRACTION	r_nbd_refined	0.184	0.2	1121
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.223	0.2	6833
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	3990
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	3851
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.153	0.2	402
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.153	0.2	6
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.196	0.2	38
X-RAY DIFFRACTION	r_nbd_other	0.302	0.2	138
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.271	0.2	29
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.081	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	1.513	2.141	4392
X-RAY DIFFRACTION	r_mcbond_other	1.512	2.141	4391
X-RAY DIFFRACTION	r_mcangle_it	2.464	3.195	5476
X-RAY DIFFRACTION	r_mcangle_other	2.464	3.195	5477
X-RAY DIFFRACTION	r_scbond_it	2.008	2.37	4147
X-RAY DIFFRACTION	r_scbond_other	1.804	2.302	4084
X-RAY DIFFRACTION	r_scangle_it	3.133	3.473	6170
X-RAY DIFFRACTION	r_scangle_other	2.93	3.372	6079
X-RAY DIFFRACTION	r_lrange_it	5.94	24.895	8634
X-RAY DIFFRACTION	r_lrange_other	5.861	24.558	8562
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.119	0.05	6080
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.105	0.05	3633
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.123	0.05	5766

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.11933	0.05007
1	2	D	X-RAY DIFFRACTION	Local ncs	0.11933	0.05007
2	3	B	X-RAY DIFFRACTION	Local ncs	0.10529	0.05007
2	4	F	X-RAY DIFFRACTION	Local ncs	0.10529	0.05007
3	5	C	X-RAY DIFFRACTION	Local ncs	0.12311	0.05007
3	6	E	X-RAY DIFFRACTION	Local ncs	0.12311	0.05007

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.1-2.151	0.3	199	0.278	4197	X-RAY DIFFRACTION	84.263
2.151-2.21	0.269	225	0.271	4452	X-RAY DIFFRACTION	93.0561
2.21-2.274	0.277	263	0.255	4541	X-RAY DIFFRACTION	96.7963
2.274-2.343	0.289	242	0.243	4571	X-RAY DIFFRACTION	98.5866
2.343-2.42	0.294	234	0.241	4269	X-RAY DIFFRACTION	98.5555
2.42-2.505	0.276	251	0.236	4170	X-RAY DIFFRACTION	97.5292
2.505-2.599	0.259	207	0.231	4011	X-RAY DIFFRACTION	96.0383
2.599-2.704	0.271	240	0.226	3927	X-RAY DIFFRACTION	99.7606
2.704-2.824	0.286	210	0.218	3766	X-RAY DIFFRACTION	99.7491
2.824-2.961	0.26	203	0.216	3595	X-RAY DIFFRACTION	99.5805
2.961-3.12	0.288	206	0.223	3421	X-RAY DIFFRACTION	99.0984
3.12-3.308	0.245	180	0.212	3257	X-RAY DIFFRACTION	98.9919
3.308-3.535	0.235	178	0.197	2985	X-RAY DIFFRACTION	97.443
3.535-3.816	0.21	165	0.189	2636	X-RAY DIFFRACTION	92.7176
3.816-4.176	0.209	166	0.172	2546	X-RAY DIFFRACTION	97.274
4.176-4.663	0.214	111	0.159	2357	X-RAY DIFFRACTION	96.4439
4.663-5.372	0.225	86	0.176	2042	X-RAY DIFFRACTION	95.6835
5.372-6.55	0.23	119	0.211	1726	X-RAY DIFFRACTION	96.8504
6.55-9.141	0.203	53	0.219	1351	X-RAY DIFFRACTION	95.5102
9.141-38.606	0.238	22	0.237	827	X-RAY DIFFRACTION	97.8111

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	0.7763	-0.0026	0.5161	3.3991	1.4307	1.2116	-0.0594	-0.026	0.0263	-0.0537	-0.1267	0.2006	0.0429	-0.0783	0.1861	0.2807	-0.0319	0.008	0.0224	-0.0234	0.2426	-16.812	-44.135	28.039
2	2.0579	-1.32	0.9919	2.9485	1.3848	3.313	-0.0345	0.01	0.0268	0.1881	0.4256	-0.6149	0.1462	0.4581	-0.3911	0.3529	0.0229	-0.1833	0.0904	-0.1179	0.5071	10.535	-34.494	52.666
3	0.9882	0.4525	0.6065	0.5911	-0.7152	3.0237	-0.0636	0.0553	0.0275	-0.0398	-0.017	-0.0609	-0.0641	0.0952	0.0805	0.2713	0.0477	-0.0522	0.0332	0.0524	0.2849	26.86	18.537	-19.547
4	0.2778	0.113	0.0052	0.568	-0.2108	1.6274	0.0228	0.0132	0.0737	-0.0369	-0.0141	-0.0734	-0.1332	-0.0301	-0.0087	0.2724	0.0242	-0.0401	0.0456	0.0568	0.2731	21.883	20.971	-16.218
5	0.7217	0.3699	1.0944	2.3473	1.4064	1.9983	0.0661	0.0789	-0.0273	0.3452	0.1145	-0.4153	0.2722	0.1448	-0.1806	0.3735	-0.0003	-0.0353	0.0181	-0.0602	0.3834	-2.282	-60.203	33.306
6	0.8232	-0.2782	0.1073	5.9273	4.2738	4.4896	0.2135	0.1679	-0.6498	1.4152	0.1781	0.0235	0.9161	0.1813	-0.3916	0.6075	0.1261	-0.24	0.0547	-0.115	0.7374	5.094	-50.448	54.069
7	1.2356	0.1984	-0.1528	2.0047	-0.8184	1.068	-0.0144	-0.0022	-0.1189	-0.0675	-0.061	-0.1861	0.0197	-0.0204	0.0754	0.2435	-0.0097	-0.0607	0.039	0.0117	0.2771	13.815	-8.348	3.841
8	2.9631	-0.3796	-0.9824	0.6377	-0.4121	1.1004	-0.0653	0.0658	-0.0819	0.0247	0.0115	-0.0219	-0.0118	-0.0791	0.0538	0.2701	-0.0072	-0.0616	0.044	-0.0104	0.2377	-16.649	-19.41	23.804
9	1.8049	0.0515	-0.5104	0.6792	-0.3131	0.5189	0.0078	-0.0026	-0.0261	0.0519	-0	0.0337	-0.087	-0.039	-0.0078	0.2499	0.0121	-0.0713	0.0822	0.0243	0.2254	0.803	9.05	3.797
10	1.1543	-0.4748	0.0462	0.8287	-0.9971	3.6054	0.0344	-0.012	0.1974	0.1947	0.0705	-0.0938	-0.0777	0.0844	-0.105	0.2747	-0.0031	-0.085	0.0375	-0.0211	0.2818	-14.112	-3.532	27.949
11	1.4529	0.3769	-1.056	1.0424	1.3918	3.7735	-0.0723	0.0241	0.1002	-0.2295	-0.1078	0.2293	-0.3579	-0.1958	0.1801	0.3602	0.0515	-0.0987	0.0242	-0.0475	0.322	-25.883	-72.515	2.643
12	0.2873	0.1875	-0.1783	0.7252	0.7018	1.3541	-0.0285	-0.0643	-0.0046	-0.1528	-0.0846	0.2129	-0.1261	0.0266	0.1131	0.3987	0.0014	-0.0652	0.0314	-0.0713	0.3254	-21.437	-74.787	6.747

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	1 - 110
2	X-RAY DIFFRACTION	2	ALL	A	111 - 209
3	X-RAY DIFFRACTION	3	ALL	B	1 - 55
4	X-RAY DIFFRACTION	4	ALL	B	56 - 129
5	X-RAY DIFFRACTION	5	ALL	C	1 - 149
6	X-RAY DIFFRACTION	6	ALL	C	150 - 219
7	X-RAY DIFFRACTION	7	ALL	D	1 - 105
8	X-RAY DIFFRACTION	8	ALL	D	106 - 210
9	X-RAY DIFFRACTION	9	ALL	E	1 - 123
10	X-RAY DIFFRACTION	10	ALL	E	124 - 220
11	X-RAY DIFFRACTION	11	ALL	F	1 - 55
12	X-RAY DIFFRACTION	12	ALL	F	56 - 129

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Protein , 2 types, 4 molecules BFCE

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Non-polymers , 3 types, 600 molecules

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Protein , 2 types, 4 molecules BFCE

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