PDB-8vk2: X-ray crystal structure of human IgE 4C8 Fab

ID or keywords:

Entry

Database: PDB / ID: 8vk2

Title

X-ray crystal structure of human IgE 4C8 Fab

Components

IgE 4C8 heavy chain
IgE 4C8 light chain

Keywords

IMMUNE SYSTEM / IgE antibody / human immune system / human IgE antibody / anti Der p 2 antibody / IgE against dust mite

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.508 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	8vk2.cif.gz	424.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8vk2.ent.gz	270.3 KB	Display	PDB format
PDBx/mmJSON format	8vk2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8vk2_validation.pdf.gz	446.4 KB	Display	wwPDB validaton report
Full document	8vk2_full_validation.pdf.gz	450.9 KB	Display
Data in XML	8vk2_validation.xml.gz	31.3 KB	Display
Data in CIF	8vk2_validation.cif.gz	44.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vk/8vk2 ftp://data.pdbj.org/pub/pdb/validation_reports/vk/8vk2	HTTPS FTP

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Related structure data

Related structure data	8vk1C 7mlhS S: Starting model for refinement C: citing same article (ref.)

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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

E: IgE 4C8 light chain

B: IgE 4C8 light chain

C: IgE 4C8 heavy chain

F: IgE 4C8 heavy chain

93.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

E: IgE 4C8 light chain

F: IgE 4C8 heavy chain

defined by author&software
46.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: IgE 4C8 light chain

C: IgE 4C8 heavy chain

defined by author&software
46.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	62.009, 80.664, 164.807
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	E
2	1	E
3	2	E
4	2	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	THR	THR	E	A	1 - 209	1 - 209
2	1	1	SER	SER	THR	THR	B	B	1 - 209	1 - 209
3	2	2	GLU	GLU	GLU	GLU	C	C	1 - 222	1 - 222
4	2	2	GLU	GLU	GLU	GLU	F	D	1 - 222	1 - 222

NCS ensembles :

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

#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: 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)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.2 Å³/Da / Density % sol: 44 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 0.1 M Tris, 0.1 M sodium formate, 20% w/v PEG3350

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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: Jul 24, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.5→39.207 Å / Num. obs: 29122 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC_1/2: 0.98 / CC star: 0.995 / R_merge(I) obs: 0.158 / R_pim(I) all: 0.064 / R_rim(I) all: 0.171 / R_sym value: 0.158 / Net I/σ(I): 16.6
Reflection shell	Resolution: 2.5→2.54 Å / Redundancy: 5.8 % / R_merge(I) obs: 0.708 / Mean I/σ(I) obs: 2 / Num. unique obs: 1423 / CC_1/2: 0.819 / CC star: 0.949 / R_pim(I) all: 0.307 / R_rim(I) all: 0.773 / R_sym value: 0.708 / % possible all: 99.9

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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: 2.508→39.207 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.918 / SU B: 27.653 / SU ML: 0.286 / Cross valid method: FREE R-VALUE / ESU R: 0.961 / ESU R Free: 0.305
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2471	1465	5.04 %
R_work	0.1978	27603	-
all	0.2	-	-
obs	-	29068	99.818 %

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: 63.554 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.1 Å²	-0 Å²	0 Å²
2-	-	-3.385 Å²	-0 Å²
3-	-	-	3.485 Å²

Refinement step

Cycle: LAST / Resolution: 2.508→39.207 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6247	0	0	190	6437

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.011	6423
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	5791
X-RAY DIFFRACTION	r_angle_refined_deg	1.22	1.657	8789
X-RAY DIFFRACTION	r_angle_other_deg	0.417	1.569	13426
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.665	5	851
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.549	5	16
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.31	10	932
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.465	10	224
X-RAY DIFFRACTION	r_chiral_restr	0.052	0.2	1009
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	7560
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1368
X-RAY DIFFRACTION	r_nbd_refined	0.2	0.2	855
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.214	0.2	5249
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	3040
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	3214
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.214	0.2	215
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.048	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.183	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.307	0.2	66
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.036	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	2.547	3.613	3416
X-RAY DIFFRACTION	r_mcbond_other	2.541	3.614	3416
X-RAY DIFFRACTION	r_mcangle_it	4.031	6.486	4263
X-RAY DIFFRACTION	r_mcangle_other	4.032	6.487	4264
X-RAY DIFFRACTION	r_scbond_it	2.995	3.848	3007
X-RAY DIFFRACTION	r_scbond_other	2.994	3.849	3008
X-RAY DIFFRACTION	r_scangle_it	4.714	6.953	4526
X-RAY DIFFRACTION	r_scangle_other	4.714	6.954	4527
X-RAY DIFFRACTION	r_lrange_it	7.924	44.498	25936
X-RAY DIFFRACTION	r_lrange_other	7.917	44.455	25889
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.103	0.05	6066
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.106	0.05	6140

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	0.10301	0.05009
1	2	E	X-RAY DIFFRACTION	Local ncs	0.10301	0.05009
2	3	E	X-RAY DIFFRACTION	Local ncs	0.10596	0.05009
2	4	E	X-RAY DIFFRACTION	Local ncs	0.10596	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
2.508-2.572	0.342	90	0.3	1984	0.302	2095	0.92	0.95	98.9976	0.269
2.572-2.643	0.333	109	0.268	1944	0.271	2053	0.923	0.961	100	0.24
2.643-2.719	0.303	101	0.248	1907	0.251	2008	0.942	0.964	100	0.216
2.719-2.802	0.314	103	0.25	1845	0.253	1949	0.939	0.961	99.9487	0.221
2.802-2.894	0.34	81	0.248	1807	0.253	1888	0.922	0.961	100	0.22
2.894-2.995	0.319	82	0.233	1769	0.236	1852	0.93	0.965	99.946	0.204
2.995-3.107	0.277	89	0.222	1673	0.225	1762	0.954	0.97	100	0.196
3.107-3.233	0.292	78	0.225	1616	0.228	1694	0.948	0.97	100	0.201
3.233-3.376	0.263	68	0.204	1567	0.206	1635	0.958	0.976	100	0.185
3.376-3.539	0.23	103	0.195	1472	0.197	1575	0.971	0.978	100	0.177
3.539-3.729	0.25	77	0.181	1418	0.184	1495	0.959	0.981	100	0.164
3.729-3.953	0.233	78	0.174	1352	0.177	1431	0.972	0.982	99.9301	0.162
3.953-4.223	0.233	71	0.15	1277	0.154	1348	0.965	0.987	100	0.142
4.223-4.557	0.164	63	0.143	1173	0.145	1241	0.983	0.987	99.5971	0.138
4.557-4.985	0.18	71	0.144	1100	0.146	1171	0.983	0.988	100	0.138
4.985-5.562	0.215	59	0.16	1011	0.163	1071	0.967	0.986	99.9066	0.156
5.562-6.401	0.218	46	0.195	900	0.197	946	0.974	0.977	100	0.186
6.401-7.788	0.223	38	0.198	783	0.199	823	0.968	0.975	99.757	0.196
7.788-10.802	0.227	35	0.189	610	0.191	651	0.964	0.982	99.0783	0.193
10.802-39.207	0.302	23	0.312	395	0.312	421	0.958	0.948	99.2874	0.315

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	3.5336	-0.1009	0.6865	1.9126	1.1528	3.9345	0.2646	-0.1441	-0.1322	0.0017	-0.184	0.0982	-0.1762	-0.3004	-0.0807	0.2051	0.0977	-0.0391	0.7782	-0.0477	0.0235	-21.328	30.583	-20.449
2	2.9167	-2.029	1.58	1.6445	-0.6451	1.7826	0.0382	0.1309	-0.1056	0.0152	-0.0628	0.1068	0.1086	-0.0143	0.0246	0.166	0.0039	0.0105	0.6103	0.0176	0.0554	4.953	13.053	-32.328
3	3.5709	-0.5263	0.6941	1.9194	-0.7648	5.0404	0.1535	-0.1483	-0.366	-0.1281	-0.0427	-0.0155	0.1761	0.0199	-0.1108	0.0799	-0.0498	-0.0272	0.6205	0.129	0.0619	21.475	32.191	-65.932
4	6.1391	2.0121	2.8701	1.9474	0.7374	3.5665	0.2149	0.0925	-0.4013	-0.0738	-0.1585	-0.16	0.6594	0.2158	-0.0564	0.2584	0.0731	0.0276	0.5409	-0.0101	0.0499	-6.739	13.843	-55.686
5	5.7093	1.6472	-1.2873	0.9346	-1.3711	2.53	-0.0311	0.0484	-0.1174	-0.1272	-0.0085	-0.0445	0.1921	-0.0878	0.0396	0.1577	0.0235	0.015	0.5823	0.0122	0.0047	8.029	37.663	-82.1
6	2.408	-0.4389	-0.3259	0.6518	-0.7984	5.6289	-0.1723	0.2282	0.0362	-0.0703	-0.0853	0.0485	0.0865	-0.1786	0.2576	0.204	-0.035	-0.0238	0.6971	-0.0083	0.0338	-18.239	25.899	-56.868
7	3.383	-0.6432	0.2937	1.8003	0.8498	3.1382	0.1231	-0.2169	-0.0464	0.1121	-0.1474	-0.0641	0.0072	-0.3843	0.0242	0.1853	-0.0111	-0.0278	0.725	-0.0437	0.011	-7.626	33.858	-3.854
8	2.4505	-0.7242	0.6886	1.5866	-1.7844	7.9126	-0.2488	0.1025	0.4477	0.1885	-0.2293	-0.3547	-0.0883	0.4544	0.4781	0.0666	-0.0176	-0.0426	0.563	0.1108	0.1563	18.275	23.111	-30.409

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	E	1 - 101
2	X-RAY DIFFRACTION	2	ALL	E	102 - 209

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