PDB-6eyn: Structure of the 8D6 (anti-IgE) Fab

ID or keywords:

Entry

Database: PDB / ID: 6eyn

Title

Structure of the 8D6 (anti-IgE) Fab

Components

8D6 Fab heavy chain
8D6 Fab light chain

Keywords

IMMUNE SYSTEM / Immunoglobulin E / Fab / antibody

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Chen, J.B. / Ramadani, F. / Pang, M.O.Y. / Beavil, R.L. / Holdom, M.D. / Mitropoulou, A.N. / Beavil, A.J. / Gould, H.J. / Chang, T.W. / Sutton, B.J. ...

Funding support

United Kingdom, 3items

Citation

Journal: Sci Rep / Year: 2018
Title: Structural basis for selective inhibition of immunoglobulin E-receptor interactions by an anti-IgE antibody.
Authors: Chen, J.B. / Ramadani, F. / Pang, M.O.Y. / Beavil, R.L. / Holdom, M.D. / Mitropoulou, A.N. / Beavil, A.J. / Gould, H.J. / Chang, T.W. / Sutton, B.J. / McDonnell, J.M. / Davies, A.M.

History

Deposition	Nov 13, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 15, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6eyn.cif.gz	486.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6eyn.ent.gz	403.8 KB	Display	PDB format
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Validation report

Summary document	6eyn_validation.pdf.gz	497.5 KB	Display	wwPDB validaton report
Full document	6eyn_full_validation.pdf.gz	504.9 KB	Display
Data in XML	6eyn_validation.xml.gz	44.7 KB	Display
Data in CIF	6eyn_validation.cif.gz	62.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ey/6eyn ftp://data.pdbj.org/pub/pdb/validation_reports/ey/6eyn	HTTPS FTP

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Related structure data

Related structure data	6eyoC 1i7zS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3vfg-d 5mp5-2 6y1n-d 5alc-d 4gay-2 5tjd-d 6x1u-2 5dmg-3 4yhm-d 2v7h-1 4jzo-1 6elj-2 1ejo-d 4j1u-2 3qg7-d 6p8d-2 1bfo-2 4yhn-2 1nc2-2 7k8n-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

6eyoC

1i7zS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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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

L: 8D6 Fab light chain

H: 8D6 Fab heavy chain

A: 8D6 Fab light chain

B: 8D6 Fab heavy chain

C: 8D6 Fab light chain

D: 8D6 Fab heavy chain

hetero molecules

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

1

L: 8D6 Fab light chain

H: 8D6 Fab heavy chain

hetero molecules

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

2

A: 8D6 Fab light chain

B: 8D6 Fab heavy chain

hetero molecules

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

3

C: 8D6 Fab light chain

D: 8D6 Fab heavy chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	157.957, 157.957, 77.503
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	78
Space group name H-M	P4₃

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Antibody , 2 types, 6 molecules LACHBD

#1: Antibody	8D6 Fab light chain Mass: 23803.211 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: 8D6 Fab light chain / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody	8D6 Fab heavy chain Mass: 24555.291 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: 8D6 Fab heavy chain / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 262 molecules

#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 3.44 Å³/Da / Density % sol: 64.25 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M ADA (N-(2-acetamido) iminodiacetic acid) pH6.5 and 12% (w/v) PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.4→70.64 Å / Num. obs: 74039 / % possible obs: 98.8 % / Redundancy: 6.2 % / CC_1/2: 0.996 / R_merge(I) obs: 0.123 / R_pim(I) all: 0.049 / Net I/σ(I): 10.5
Reflection shell	Resolution: 2.4→2.45 Å / Redundancy: 6.3 % / R_merge(I) obs: 1.47 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4617 / CC_1/2: 0.643 / R_pim(I) all: 0.581 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1I7Z

1i7z

Resolution: 2.4→43.553 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.63

	R_factor	Num. reflection	% reflection
R_free	0.2121	3694	4.99 %
R_work	0.1813	-	-
obs	0.1828	73961	98.68 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.4→43.553 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9109	0	59	249	9417

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	9451
X-RAY DIFFRACTION	f_angle_d	0.643	12910
X-RAY DIFFRACTION	f_dihedral_angle_d	13.466	5516
X-RAY DIFFRACTION	f_chiral_restr	0.045	1431
X-RAY DIFFRACTION	f_plane_restr	0.004	1671

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 (%)
2.4001-2.4317	0.3434	147	0.2894	2744	X-RAY DIFFRACTION	100
2.4317-2.465	0.3313	144	0.2823	2715	X-RAY DIFFRACTION	100
2.465-2.5002	0.3264	144	0.2772	2719	X-RAY DIFFRACTION	100
2.5002-2.5375	0.2958	144	0.2512	2690	X-RAY DIFFRACTION	100
2.5375-2.5771	0.2482	146	0.242	2720	X-RAY DIFFRACTION	100
2.5771-2.6194	0.2823	142	0.2328	2716	X-RAY DIFFRACTION	100
2.6194-2.6645	0.2918	143	0.2336	2751	X-RAY DIFFRACTION	100
2.6645-2.713	0.2865	141	0.2266	2696	X-RAY DIFFRACTION	100
2.713-2.7652	0.255	145	0.2195	2736	X-RAY DIFFRACTION	100
2.7652-2.8216	0.2649	144	0.2249	2691	X-RAY DIFFRACTION	100
2.8216-2.8829	0.3271	147	0.2394	2755	X-RAY DIFFRACTION	100
2.8829-2.95	0.2688	142	0.2338	2700	X-RAY DIFFRACTION	100
2.95-3.0237	0.271	144	0.2282	2732	X-RAY DIFFRACTION	100
3.0237-3.1055	0.269	144	0.2052	2721	X-RAY DIFFRACTION	100
3.1055-3.1968	0.212	138	0.1997	2761	X-RAY DIFFRACTION	100
3.1968-3.3	0.2261	144	0.1874	2691	X-RAY DIFFRACTION	100
3.3-3.4179	0.2025	141	0.1869	2751	X-RAY DIFFRACTION	100
3.4179-3.5547	0.1964	145	0.1797	2713	X-RAY DIFFRACTION	100
3.5547-3.7164	0.1724	141	0.1632	2744	X-RAY DIFFRACTION	100
3.7164-3.9122	0.186	140	0.1616	2751	X-RAY DIFFRACTION	100
3.9122-4.1571	0.1855	147	0.1515	2742	X-RAY DIFFRACTION	100
4.1571-4.4778	0.1478	147	0.1321	2737	X-RAY DIFFRACTION	100
4.4778-4.9278	0.1595	144	0.1276	2758	X-RAY DIFFRACTION	100
4.9278-5.6396	0.1734	144	0.1421	2764	X-RAY DIFFRACTION	100
5.6396-7.1003	0.1961	143	0.1828	2765	X-RAY DIFFRACTION	99
7.1003-43.5597	0.2433	103	0.2063	2004	X-RAY DIFFRACTION	70

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	3.0595	1.1741	-0.3222	2.8229	-1.725	5.104	0.0307	0.2455	-0.6136	-0.2482	0.0837	-0.2118	0.646	0.2096	-0.1047	0.448	-0.0084	-0.1262	0.2854	-0.0752	0.474	228.7356	112.9172	-7.2852
2	0.8349	0.0625	0.3099	3.4071	-0.7857	2.3418	0.0281	-0.0378	-0.13	-0.191	0.2031	0.1181	0.0635	0.0514	-0.2133	0.1993	-0.0486	-0.0145	0.2929	0.0248	0.2943	228.9313	131.3118	-3.7676
3	1.8041	2.1373	1.9646	4.3616	3.5422	4.2477	-0.3318	0.2377	0.1819	-0.3575	0.4191	0.0498	-0.6279	0.4296	-0.076	0.5469	-0.1653	-0.0295	0.411	0.0284	0.3592	234.2253	151.4183	-4.4514
4	2.8839	1.056	-0.4985	3.2944	0.5412	1.6812	0.2035	-0.6389	0.0643	0.439	-0.2363	0.2963	0.1249	-0.7339	-0.0846	0.5666	-0.0238	-0.0548	0.5879	0.0156	0.3921	227.2432	123.5976	19.7955
5	4.0377	0.1741	0.6886	6.8331	0.7941	7.8538	0.1879	-0.3132	-0.5652	-0.1908	-0.1069	-0.397	0.3089	-0.1774	-0.1613	0.3986	0.0022	-0.1752	0.3572	0.0399	0.4446	229.9799	114.0154	11.1495
6	4.2822	-0.2763	-0.5072	1.0182	1.3554	2.1183	-0.0581	-1.3337	-1.2129	0.3194	-0.0295	-0.947	1.2819	0.1544	-0.0595	0.7974	0.0499	-0.2896	0.5148	0.1466	0.8228	232.8085	107.1624	17.5013
7	1.795	0.6572	1.3355	4.4908	1.8319	2.9519	0.3127	-0.5061	-0.3885	0.4482	-0.0956	-0.0629	0.3923	-0.3611	-0.1569	0.482	-0.039	-0.0964	0.4297	0.1002	0.3981	228.7412	118.6708	15.5775
8	2.88	0.8459	0.3503	2.8423	0.6673	4.8829	-0.0842	0.0079	0.4972	-0.1136	-0.1226	0.3421	-0.7313	-0.8155	0.2864	0.4516	0.0979	-0.0063	0.3968	-0.0021	0.3549	224.3799	151.2014	6.085
9	3.1216	0.7528	0.2161	3.5864	-0.5885	5.4632	0.1045	-0.1015	0.1479	-0.004	0.1983	0.4138	-0.0641	-0.9685	-0.2864	0.3953	-0.0057	0.0437	0.4374	0.0439	0.3522	222.1862	144.4303	6.9952
10	3.8773	-0.1807	1.485	5.0691	-1.1979	4.5486	-0.3104	-0.5486	0.7499	0.1645	0.4741	0.3833	-0.9455	-1.3438	0.0408	0.7035	0.1456	0.1353	0.6621	-0.0704	0.623	218.7907	151.8376	12.3084
11	2.1827	0.4117	-0.2438	2.0748	0.2393	1.5557	0.1133	0.4793	-0.159	-0.7632	-0.3361	0.3953	0.0831	-0.1661	0.2644	0.6295	0.3132	-0.0613	0.7235	0.0456	0.7266	256.2975	112.1674	-5.1667
12	2.5271	-1.0261	-1.9247	3.3691	-0.5888	2.1256	0.3965	0.5663	-0.0657	-0.6991	-0.6168	0.0719	-0.0079	0.1413	0.2371	0.6718	0.353	0.0311	0.6856	0.1334	0.6146	264.5632	113.4693	-4.7726
13	2.2107	-1.9911	-0.4743	3.7292	-1.0057	2.5339	0.0054	-0.0667	0.3027	-0.1067	-0.3348	-0.4234	-0.0896	0.0794	0.3745	0.3425	0.1167	-0.0753	0.5564	0.1101	0.623	259.0919	116.5553	11.7187
14	2.7473	-0.1567	-0.2562	2.9971	-0.8262	2.5538	-0.5076	-0.6392	-0.0042	0.6719	0.147	-0.1981	-0.2752	-0.0741	0.3381	0.5713	0.2345	-0.0762	0.777	0.0879	0.5206	254.5243	115.545	27.4357
15	1.3835	-0.4583	-0.983	2.3569	1.6505	1.4948	-0.6543	-0.778	-0.0924	1.5876	-0.0462	0.1986	-0.6116	-0.5577	0.5038	1.416	0.557	-0.1019	1.2214	-0.0319	0.5497	250.6168	120.459	38.0524
16	2.744	-0.0061	-0.6646	6.6877	3.7023	4.493	-0.3967	-0.9766	-0.3262	1.0185	-0.1845	-0.0219	-0.0075	-0.3806	0.5657	0.8655	0.3438	0.0077	1.0115	0.156	0.5062	255.6814	109.5375	37.2608
17	2.8708	0.9883	-0.0995	1.0582	-0.1557	1.8565	0.0413	-0.1378	1.3272	-0.3375	-0.133	-1.2715	0.046	0.8437	0.0139	0.4553	0.0752	0.1077	0.6247	0.165	1.1438	260.5939	139.9589	2.7086
18	2.3498	-0.643	-0.0148	4.1211	1.1659	4.1039	0.3047	0.5576	0.4303	-0.1519	-0.5287	-0.6104	0.0571	-0.0109	0.1151	0.5663	0.2453	0.17	0.6088	0.2547	0.6951	256.4223	131.1513	-4.4768
19	2.7242	-0.1963	-1.7909	2.2476	0.9913	2.7787	0.5981	0.8165	1.1346	-0.8398	-0.389	-0.3427	-0.7034	-0.3012	-0.2023	0.7228	0.2836	0.2157	0.6279	0.2787	0.8906	256.6093	140.1563	-8.0921
20	1.8939	-1.7795	-0.4495	3.1255	0.9752	2.8422	0.4893	0.1913	0.748	-0.4521	-0.4841	-0.866	-0.0094	0.373	0.1369	0.4619	0.1526	0.0393	0.5313	0.1701	0.788	258.0156	133.2639	1.4092
21	1.7992	-0.2711	-0.3209	1.0985	-1.0382	1.6982	-0.4362	-0.5373	0.4842	0.8332	-0.0853	-1.2927	-0.0286	0.6847	0.3108	0.6365	0.1349	-0.4435	0.8195	0.0107	0.9954	263.5974	127.1139	27.0049
22	2.7466	-0.3812	0.0169	0.5622	0.8521	1.449	-0.3279	-0.2781	1.0631	1.0849	-0.036	-1.1586	-0.3155	1.2346	0.0601	0.929	0.0463	-0.5677	0.9834	-0.1143	1.497	266.3884	135.7708	26.159
23	3.3897	0.9828	0.8773	5.4213	-0.3703	4.3043	-0.0827	0.3321	-0.0794	-0.5617	0.3298	0.1742	0.536	-0.1227	-0.1989	0.5514	-0.1787	-0.1064	0.4487	0.0552	0.3597	217.8274	131.1161	-34.6683
24	1.2973	0.2122	-0.3348	2.0934	0.6988	1.3668	0.2901	0.2676	0.1365	-0.5539	0.1589	1.6083	0.1529	-0.9096	-0.1402	0.7032	-0.3537	-0.5028	1.2152	0.577	1.6044	183.4071	129.0002	-39.7116
25	4.921	0.2896	-1.0123	3.0985	0.485	1.6596	-0.0898	-0.3444	0.4158	0.0382	0.1213	0.5329	-0.3333	-0.3725	-0.0203	0.6352	-0.0949	-0.0741	0.5114	0.1986	0.5647	211.8704	153.3313	-29.9134
26	3.8252	-0.4071	-0.6914	4.1659	-0.6602	4.4664	-0.1865	0.5702	0.0781	-0.8832	0.2397	0.4812	-0.6265	-0.1398	-0.0649	0.7346	-0.1497	-0.086	0.5212	0.1501	0.4946	217.993	152.972	-38.8984
27	3.8379	0.0105	0.6084	3.2181	-0.4154	1.4829	-0.2339	0.1742	0.4443	-0.1493	0.2929	0.859	-0.385	-0.3554	0.0167	0.633	-0.0953	-0.1118	0.5224	0.1828	0.6054	210.746	151.5467	-33.8472
28	1.5467	0.5901	0.2918	4.0268	1.2238	0.3737	0.0631	-0.0562	0.8149	0.4074	-0.0119	1.6406	-0.1092	-0.4423	-0.0813	0.739	-0.1153	-0.0172	1.0535	0.382	1.4628	186.0339	143.3217	-31.4221

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'L' and (resid 1 through 79 )
2	X-RAY DIFFRACTION	2	chain 'L' and (resid 80 through 132 )
3	X-RAY DIFFRACTION	3	chain 'L' and (resid 133 through 217 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 2 through 25 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 29 through 52 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 53 through 64 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 65 through 125 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 126 through 151 )
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 152 through 209 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 210 through 221 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 1 through 42 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 43 through 79 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 80 through 132 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 133 through 178 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 179 through 202 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 203 through 216 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 2 through 31 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 32 through 52 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 53 through 83 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 84 through 125 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 126 through 200 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 201 through 219 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 1 through 105 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 106 through 212 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 1 through 39 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 40 through 73 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 74 through 125 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 126 through 211 )

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