PDB-8vk1: X-ray crystal structure of human IgE 4C8 Fab complex with Der p 2.0103

ID or keywords:

Entry

Database: PDB / ID: 8vk1

Title

X-ray crystal structure of human IgE 4C8 Fab complex with Der p 2.0103

Components

Der p 2 variant 3
IgE 4C8 heavy chain
IgE 4C8 light chain

Keywords

ALLERGEN/IMMUNE SYSTEM / dust mite allergy / house dust mite / Der p 2-IgE complex / Human IgE against Der p 2 / antibody-allergen complex / antibody-allergen interaction / 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. / intracellular cholesterol transport / cholesterol efflux / cholesterol binding / 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: 3.05 Å

Authors

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

Funding support

United States, 1items

Citation

Journal: J.Allergy Clin.Immunol. / Year: 2024
Title: Structural analysis of human IgE monoclonal antibody epitopes on dust mite allergen Der p 2.
Authors: Ball, A. / Khatri, K. / Glesner, J. / Vailes, L.D. / Wunschmann, S. / Gabel, S.A. / Mueller, G.A. / Zhang, J. / Peebles Jr., R.S. / Chapman, M.D. / Smith, S.A. / Chruszcz, M. / Pomes, A.

History

Deposition	Jan 8, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 19, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8vk1.cif.gz	554.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8vk1.ent.gz	359.1 KB	Display	PDB format
PDBx/mmJSON format	8vk1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8vk1_validation.pdf.gz	452.1 KB	Display	wwPDB validaton report
Full document	8vk1_full_validation.pdf.gz	459.2 KB	Display
Data in XML	8vk1_validation.xml.gz	38.5 KB	Display
Data in CIF	8vk1_validation.cif.gz	54 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vk/8vk1 ftp://data.pdbj.org/pub/pdb/validation_reports/vk/8vk1	HTTPS FTP

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Related structure data

Related structure data	8vk2C 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	#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

E: IgE 4C8 light chain

D: Der p 2 variant 3

F: IgE 4C8 heavy chain

B: IgE 4C8 light chain

C: IgE 4C8 heavy chain

A: Der p 2 variant 3

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

1

E: IgE 4C8 light chain

D: Der p 2 variant 3

F: IgE 4C8 heavy chain

defined by author
Evidence: surface plasmon resonance
61.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: IgE 4C8 light chain

C: IgE 4C8 heavy chain

A: Der p 2 variant 3

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

Unit cell

Length a, b, c (Å)	225.254, 95.298, 69.209
Angle α, β, γ (deg.)	90.000, 105.724, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	C-307- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	E
2	1	E
3	2	E
4	2	E
5	3	E
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	SER	SER	GLU	GLU	E	A	1 - 210	1 - 210
2	1	1	SER	SER	GLU	GLU	B	D	1 - 210	1 - 210
3	2	2	ASP	ASP	ASP	ASP	D	B	1 - 129	1 - 129
4	2	2	ASP	ASP	ASP	ASP	A	F	1 - 129	1 - 129
5	3	3	GLU	GLU	LYS	LYS	F	C	1 - 224	1 - 224
6	3	3	GLU	GLU	LYS	LYS	C	E	1 - 224	1 - 224

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

#1: Antibody	IgE 4C8 light chain Mass: 22562.857 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)
#2: Protein	Der p 2 variant 3 / Der p 2.0103 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: Antibody	IgE 4C8 heavy chain Mass: 24374.248 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)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.93 Å³/Da / Density % sol: 58 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 1.0 M lithium chloride, 0.3 M citrate, pH 4.0, 25% w/v PEG6000

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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: Feb 22, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.05→40 Å / Num. obs: 26735 / % possible obs: 99 % / Redundancy: 3.8 % / CC_1/2: 0.984 / CC star: 0.996 / R_merge(I) obs: 0.105 / R_pim(I) all: 0.061 / R_rim(I) all: 0.122 / R_sym value: 0.105 / Net I/σ(I): 13.7
Reflection shell	Resolution: 3.05→3.1 Å / R_merge(I) obs: 0.42 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1331 / CC_1/2: 0.82 / CC star: 0.949 / R_pim(I) all: 0.25 / R_rim(I) all: 0.49 / R_sym value: 0.42 / % possible all: 97.1

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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: 3.05→39.577 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.9 / WR_factor R_free: 0.237 / WR_factor R_work: 0.182 / SU B: 48.767 / SU ML: 0.376 / Average fsc free: 0.9575 / Average fsc work: 0.974 / Cross valid method: FREE R-VALUE / ESU R Free: 0.446
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2477	1353	5.077 %
R_work	0.1967	25298	-
all	0.199	-	-
obs	-	26651	98.532 %

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: 68.809 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.691 Å²	0 Å²	-1.523 Å²
2-	-	6.208 Å²	0 Å²
3-	-	-	-3.158 Å²

Refinement step

Cycle: LAST / Resolution: 3.05→39.577 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8356	0	0	59	8415

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	8557
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	7834
X-RAY DIFFRACTION	r_angle_refined_deg	1.302	1.799	11682
X-RAY DIFFRACTION	r_angle_other_deg	0.448	1.734	18185
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.291	5	1123
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.174	5	20
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.907	10	1319
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.338	10	310
X-RAY DIFFRACTION	r_chiral_restr	0.057	0.2	1339
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	9975
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1765
X-RAY DIFFRACTION	r_nbd_refined	0.205	0.2	1314
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.218	0.2	7076
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.2	4118
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	4231
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.226	0.2	228
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.024	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.256	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.27	0.2	51
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.431	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	2.078	2.517	4510
X-RAY DIFFRACTION	r_mcbond_other	2.078	2.517	4510
X-RAY DIFFRACTION	r_mcangle_it	3.576	4.517	5627
X-RAY DIFFRACTION	r_mcangle_other	3.576	4.517	5628
X-RAY DIFFRACTION	r_scbond_it	2.02	2.593	4047
X-RAY DIFFRACTION	r_scbond_other	2.02	2.593	4046
X-RAY DIFFRACTION	r_scangle_it	3.465	4.699	6055
X-RAY DIFFRACTION	r_scangle_other	3.465	4.699	6056
X-RAY DIFFRACTION	r_lrange_it	7.535	30.032	33760
X-RAY DIFFRACTION	r_lrange_other	7.535	30.031	33761
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.144	0.05	5882
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.128	0.05	3548
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.118	0.05	6322

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	E	X-RAY DIFFRACTION	Local ncs	0.14434	0.05008
1	2	E	X-RAY DIFFRACTION	Local ncs	0.14434	0.05008
2	3	E	X-RAY DIFFRACTION	Local ncs	0.1277	0.05008
2	4	E	X-RAY DIFFRACTION	Local ncs	0.1277	0.05008
3	5	E	X-RAY DIFFRACTION	Local ncs	0.11835	0.05009
3	6	E	X-RAY DIFFRACTION	Local ncs	0.11835	0.05009

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
3.05-3.129	0.428	90	0.32	1736	0.325	1989	0.912	0.951	91.8049	0.286
3.129-3.214	0.321	101	0.279	1790	0.281	1913	0.943	0.96	98.85	0.245
3.214-3.306	0.247	96	0.246	1766	0.246	1874	0.959	0.968	99.3597	0.219
3.306-3.407	0.258	96	0.236	1689	0.237	1801	0.965	0.969	99.1116	0.209
3.407-3.518	0.318	85	0.23	1671	0.234	1782	0.947	0.971	98.541	0.203
3.518-3.641	0.305	72	0.235	1622	0.238	1724	0.941	0.968	98.2599	0.213
3.641-3.777	0.275	89	0.236	1543	0.238	1634	0.949	0.968	99.8776	0.215
3.777-3.93	0.28	94	0.211	1495	0.215	1591	0.944	0.973	99.8743	0.187
3.93-4.103	0.282	85	0.187	1458	0.192	1544	0.956	0.978	99.9352	0.174
4.103-4.301	0.221	71	0.168	1368	0.171	1445	0.973	0.983	99.5848	0.157
4.301-4.53	0.162	78	0.143	1323	0.144	1409	0.984	0.988	99.4322	0.134
4.53-4.801	0.184	46	0.148	1247	0.149	1304	0.978	0.988	99.1564	0.141
4.801-5.127	0.18	58	0.146	1158	0.148	1242	0.983	0.988	97.9066	0.143
5.127-5.53	0.183	53	0.152	1093	0.154	1167	0.98	0.987	98.2005	0.145
5.53-6.046	0.23	36	0.164	1013	0.166	1052	0.973	0.984	99.7148	0.158
6.046-6.74	0.245	59	0.198	926	0.2	986	0.963	0.977	99.8986	0.193
6.74-7.746	0.279	53	0.193	820	0.199	878	0.959	0.977	99.4305	0.196
7.746-9.397	0.175	33	0.172	695	0.172	737	0.979	0.982	98.7788	0.181
9.397-12.93	0.22	36	0.172	533	0.176	582	0.976	0.985	97.7663	0.187
12.93-39.577	0.317	22	0.272	349	0.275	373	0.942	0.962	99.4638	0.303

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	3.1703	1.1036	1.0042	4.7563	0.6419	1.4704	-0.2171	0.0057	0.0745	0.1294	0.051	-0.22	-0.0661	0.1412	0.1661	0.8293	0.1055	0.1221	0.0394	-0.0227	0.437	31.065	82.834	55.461
2	3.7943	0.4886	0.51	5.3849	0.5827	2.2151	0.055	-0.4112	-0.1906	0.8328	-0.3607	0.2068	0.3254	0.0263	0.3057	0.9219	0.0307	0.1706	0.0752	0.0242	0.3891	26.985	80.491	60.91
3	1.5241	0.5691	-0.2663	4.6745	-0.3544	1.9478	0.0982	-0.3026	0.1525	0.2342	-0.004	-0.3394	0.1357	0.0481	-0.0941	0.8059	-0.006	0.1632	0.1188	-0.2128	0.6413	28.388	116.986	56.978
4	5.9879	-1.0495	-1.8529	1.7271	0.7174	2.6391	-0.064	-0.4696	-0.0662	0.1878	-0.1125	-0.1904	-0.0575	0.1984	0.1765	0.7587	-0.018	0.1857	0.0672	0.0561	0.4715	6.709	146.11	60.447
5	1.5013	-2.0304	0.2252	3.0035	-0.3402	0.0529	-0.1434	0.0774	-0.1317	0.3768	0.0704	0.1928	-0.0254	-0.0238	0.0731	0.9334	0.0175	0.2284	0.1387	-0.0784	0.632	7.541	111.149	54.54
6	3.013	-0.1118	1.157	3.2671	-1.1935	3.8372	0.0477	0.15	0.0106	-0.2113	-0.1528	-0.0111	-0.1978	0.2199	0.1051	0.7744	-0.0016	0.2649	0.0442	-0.0524	0.4111	-1.78	140.705	46.9
7	3.4823	-2.9216	0.8048	22.9499	14.2155	11.0829	-0.7746	-0.1197	-0.2767	0.5887	0.4086	0.9526	-0.06	0.3065	0.366	1.0339	0.0495	0.1813	0.284	-0.0394	0.7086	30.956	91.749	37.745
8	3.6915	-1.3512	-0.2354	3.5435	0.1964	1.16	0.1122	-0.1529	0.4487	-0.1802	-0.1817	-0.1636	-0.1913	-0.1601	0.0695	0.8641	-0.0234	0.1484	0.0525	-0.0699	0.6826	36.208	97.819	30.163
9	1.0109	0.965	0.0477	1.3827	0.2353	0.669	0.0516	0.0108	-0.0265	0.1216	-0.002	-0.103	0.0905	0.0781	-0.0496	0.8923	0.0479	0.1641	0.0165	-0.0302	0.6038	30.424	54.788	29.774
10	2.6575	1.0681	3.4036	3.4191	1.8713	7.2706	-0.0596	0.859	0.1052	0.1364	-0.0343	-0.5479	-0.1232	0.955	0.094	0.7125	-0.05	0.1982	0.3435	0.0222	0.628	20.382	32.439	17.5
11	1.0918	1.5837	0.1148	2.4623	-0.0792	0.4099	-0.1291	-0.0032	0.1163	-0.0892	0.0403	0.186	-0.0277	-0.0775	0.0888	0.8149	0.0157	0.1895	0.0176	-0.0465	0.5607	15.935	67.496	24.093
12	4.2445	1.0604	-0.9339	4.8465	-2.2765	1.7381	-0.0989	-0.0935	-0.1188	0.0799	-0.0821	0.0836	-0.0248	-0.0101	0.1809	0.8031	-0.0127	0.1791	0.0129	-0.0561	0.3823	4.269	37.46	25.621

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	9	ALL	E	1 - 138
2	X-RAY DIFFRACTION	10	ALL	E	139 - 210

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