PDB-6qn7: Structure of bovine anti-RSV hybrid Fab B4HC-B13LC

ID or keywords:

Entry

Database: PDB / ID: 6qn7

Title

Structure of bovine anti-RSV hybrid Fab B4HC-B13LC

Components

Heavy chain of bovine anti-RSV B4
Light chain of bovine anti-RSV B13

Keywords

IMMUNE SYSTEM / cattle antibodies / bovine respiratory syncytial virus / RSV / Fab / hybrid Fab

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Bos taurus (domestic cattle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Ren, J. / Nettleship, J.E. / Harris, G. / Mwangi, W. / Rhaman, N. / Grant, C. / Kotecha, A. / Fry, E. / Charleston, B. / Stuart, D.I. ...

Funding support

United Kingdom, 1items

Citation

Journal: Mol.Immunol. / Year: 2019
Title: The role of the light chain in the structure and binding activity of two cattle antibodies that neutralize bovine respiratory syncytial virus.
Authors: Ren, J. / Nettleship, J.E. / Harris, G. / Mwangi, W. / Rhaman, N. / Grant, C. / Kotecha, A. / Fry, E. / Charleston, B. / Stuart, D.I. / Hammond, J. / Owens, R.J.

History

Deposition	Feb 10, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 29, 2019	Provider: repository / Type: Initial release
Revision 1.1	Aug 21, 2019	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2	Nov 13, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6qn7.cif.gz	342.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6qn7.ent.gz	281.3 KB	Display	PDB format
PDBx/mmJSON format	6qn7.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/qn/6qn7 ftp://data.pdbj.org/pub/pdb/validation_reports/qn/6qn7	HTTPS FTP

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Related structure data

Related structure data	6qn8C 6qn9C 6qnaC C: citing same article (ref.)
Similar structure data	4llu-2 4kkc-3 5i1h-d 5gz0-1 1um5-d 3cfk-1 1uyw-2 2gcy-d 7jmx-d 2gfb-3 4at6-2 5i1a-2 6bpb-d 5b6f-3 6xtg-d 6nfn-5 1i7z-2 3dif-1 6jwc-d 1f4y-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) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

6qn8C

6qn9C

6qnaC

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

H: Heavy chain of bovine anti-RSV B4

L: Light chain of bovine anti-RSV B13

A: Heavy chain of bovine anti-RSV B4

B: Light chain of bovine anti-RSV B13

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

1

H: Heavy chain of bovine anti-RSV B4

L: Light chain of bovine anti-RSV B13

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

2

A: Heavy chain of bovine anti-RSV B4

B: Light chain of bovine anti-RSV B13

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

Unit cell

Length a, b, c (Å)	42.390, 86.030, 164.960
Angle α, β, γ (deg.)	90.00, 98.62, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	Heavy chain of bovine anti-RSV B4 Mass: 25134.115 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (domestic cattle) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody	Light chain of bovine anti-RSV B13 Mass: 22635.068 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (domestic cattle) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H₂O
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: 3.11 Å³/Da / Density % sol: 60.49 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20.0% w/v Polyethylene glycol 3350 0.2 M Ammonium Chloride

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96858 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.96858 Å / Relative weight: 1
Reflection	Resolution: 2.15→76.1 Å / Num. obs: 61135 / % possible obs: 95.7 % / Redundancy: 6.1 % / CC_1/2: 1 / R_merge(I) obs: 0.094 / Net I/σ(I): 10.3
Reflection shell	Resolution: 2.15→2.19 Å / Redundancy: 3.7 % / Num. unique obs: 2316 / CC_1/2: 0.55 / % possible all: 72.4

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Processing

Software

Name	Version	Classification
PHENIX	(dev_3386: ???)	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.15→45.958 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.32

	R_factor	Num. reflection	% reflection
R_free	0.234	2912	4.77 %
R_work	0.2026	-	-
obs	0.2041	61097	95.65 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.15→45.958 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6396	0	0	335	6731

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6534
X-RAY DIFFRACTION	f_angle_d	0.912	8913
X-RAY DIFFRACTION	f_dihedral_angle_d	13.019	3949
X-RAY DIFFRACTION	f_chiral_restr	0.058	1059
X-RAY DIFFRACTION	f_plane_restr	0.006	1126

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 (%)
2.1501-2.1853	0.3663	104	0.3173	2091	X-RAY DIFFRACTION	72
2.1853-2.223	0.3537	113	0.3083	2219	X-RAY DIFFRACTION	77
2.223-2.2634	0.3435	126	0.2999	2411	X-RAY DIFFRACTION	84
2.2634-2.3069	0.3092	135	0.3008	2547	X-RAY DIFFRACTION	90
2.3069-2.354	0.3437	141	0.2873	2704	X-RAY DIFFRACTION	92
2.354-2.4052	0.3069	127	0.2749	2826	X-RAY DIFFRACTION	99
2.4052-2.4612	0.3547	126	0.2629	2930	X-RAY DIFFRACTION	99
2.4612-2.5227	0.3251	129	0.2607	2880	X-RAY DIFFRACTION	100
2.5227-2.5909	0.288	120	0.2497	2850	X-RAY DIFFRACTION	99
2.5909-2.6671	0.3042	140	0.254	2899	X-RAY DIFFRACTION	100
2.6671-2.7532	0.2682	145	0.2367	2875	X-RAY DIFFRACTION	100
2.7532-2.8516	0.2812	131	0.2172	2891	X-RAY DIFFRACTION	100
2.8516-2.9658	0.2344	149	0.2099	2865	X-RAY DIFFRACTION	100
2.9658-3.1007	0.2376	178	0.2154	2868	X-RAY DIFFRACTION	100
3.1007-3.2641	0.2431	172	0.2092	2890	X-RAY DIFFRACTION	100
3.2641-3.4686	0.2522	138	0.2109	2849	X-RAY DIFFRACTION	100
3.4686-3.7363	0.2262	144	0.1904	2889	X-RAY DIFFRACTION	100
3.7363-4.1121	0.1931	168	0.1774	2891	X-RAY DIFFRACTION	100
4.1121-4.7066	0.1617	130	0.1463	2933	X-RAY DIFFRACTION	100
4.7066-5.9278	0.1765	132	0.1599	2923	X-RAY DIFFRACTION	100
5.9278-45.9685	0.2215	164	0.1874	2954	X-RAY DIFFRACTION	99

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	0.0157	-0.6378	0.1058	4.3982	1.8728	4.0189	0.3195	0.5325	0.1828	-0.7888	-0.0437	-0.1772	-0.6733	-0.0248	-0.1601	0.4973	-0.0513	0.0323	0.4847	-0.0818	0.3042	45.342	34.7004	69.2115
2	2.9291	-0.2881	-0.8266	2.7667	-0.7596	3.2638	0.1109	0.0793	0.1526	-0.0556	0.0339	0.1291	-0.3828	0.0013	-0.0153	0.35	-0.001	0.0175	0.358	-0.1124	0.3461	43.2348	36.5899	79.8965
3	4.4978	-0.3416	-0.0403	2.85	-2.5098	4.9107	-0.1261	-0.1413	0.0641	0.4371	0.1686	-0.4157	0.5794	0.1747	0.1741	0.3877	-0.009	0.0576	0.3387	-0.0416	0.3548	51.0429	30.9913	83.1546
4	3.3941	1.9965	-0.1571	1.3505	-0.2246	4.1268	-0.1167	-0.0423	0.0896	-0.0225	0.3601	-0.4287	-0.2111	0.6785	-0.2302	0.3779	-0.0671	0.0119	0.454	-0.1066	0.3351	53.0403	35.8579	75.7446
5	6.45	0.2329	-0.1788	4.834	-1.9191	1.4529	-0.0941	-0.5564	-0.0341	1.1871	0.1567	-0.2938	0.0504	0.2593	0.1767	0.5708	0.0289	-0.0086	0.3478	-0.0553	0.3404	43.7334	30.4534	86.5894
6	4.9753	-0.2368	2.1383	5.5976	0.5259	7.1731	0.3279	-0.3751	0.0186	1.4214	-0.0587	-0.2182	0.6334	0.621	-0.3001	0.6326	-0.0604	-0.0736	0.4589	-0.0536	0.4121	43.9274	30.2764	90.2789
7	0.0006	0.5688	0.5652	2.1102	3.486	8.2369	-0.0055	0.0308	0.1981	-0.3616	0.1229	0.0732	-0.2503	-0.0129	-0.1	0.3344	-0.0475	0.0119	0.404	-0.015	0.3264	47.4168	27.762	60.6501
8	5.7961	2.8359	-1.1619	2.3215	-2.3601	5.8443	-0.3824	0.2025	-1.106	-0.7927	0.5214	0.2629	1.6177	0.1887	-0.2206	0.785	0.1669	0.0207	0.4136	-0.0288	0.6131	43.7904	2.1729	46.0398
9	2.997	0.4026	0.3571	3.2154	1.2205	5.8158	0.0703	-0.2895	0.0132	0.0661	-0.0249	0.1097	-0.3478	-0.3606	-0.0416	0.3788	0.031	0.0868	0.2958	0.0324	0.3259	40.1273	14.3095	50.7742
10	2.559	-1.7474	-1.6682	2.0356	-0.2054	5.7838	0.4366	0.0049	-0.7255	-0.1953	-0.1767	0.2049	0.5087	-0.9789	-0.3108	0.485	0.0126	-0.0378	0.3852	0.0696	0.5134	37.0896	7.1059	46.756
11	6.1919	4.1408	0.1881	5.3472	1.2722	6.6218	-0.0866	0.1565	-0.1702	-0.1296	0.1293	0.4511	0.1621	0.0031	-0.036	0.2612	0.0712	0.0096	0.2857	0.0508	0.2663	40.3936	14.8769	42.0116
12	7.049	1.3139	0.8634	6.9283	1.9005	3.2191	0.2674	-0.5225	-0.7955	0.9715	0.0994	-1.037	0.2555	0.5239	-0.4044	0.6168	0.0211	-0.0252	0.4042	0.0779	0.5094	41.9448	10.9886	88.7701
13	5.3527	1.7521	1.1817	7.6115	0.9395	3.9955	0.0247	-0.1691	-0.113	0.3369	-0.0657	0.051	0.008	-0.135	0.0382	0.4786	0.011	0.0594	0.2661	0.014	0.2881	35.1365	17.8232	87.9425
14	0.4924	-0.4737	-0.5229	1.1739	0.2525	2.3787	-0.0663	-0.1496	0.2113	0.0487	0.0426	-0.1978	0.159	0.4104	-0.014	0.3683	0.0376	0.0319	0.3565	0.0477	0.4223	44.8764	9.551	67.9048
15	4.941	0.9776	-4.5039	2.2207	-1.2445	6.8617	-0.1145	-0.9949	-0.5654	0.0605	-0.364	-0.301	0.232	1.4373	0.3857	0.4234	0.044	0.0203	0.5974	0.1781	0.3998	47.3179	2.9751	60.3849
16	3.407	-0.3984	-0.3708	2.7559	0.9371	6.8016	0.0558	0.0692	-0.1662	-0.5124	0.0309	-0.2664	0.239	0.2303	-0.0849	0.5872	0.0526	0.0572	0.2731	-0.0177	0.3201	31.6682	4.6318	14.6319
17	2.2182	-1.1415	-0.4779	2.9832	-0.4916	6.7962	0.1377	0.1459	0.1747	-1.0046	-0.0242	-0.9138	0.1195	0.8118	-0.1125	0.6472	0.0039	0.156	0.3974	-0.0445	0.5106	34.0002	8.3461	10.8463
18	3.4495	-0.2791	-1.3029	2.185	0.4615	2.8796	-0.0169	-0.249	0.3064	0.0861	0.1349	0.2809	-0.7391	0.104	0.0931	0.5584	0.0015	-0.0007	0.31	0.0016	0.2445	13.2348	23.5249	30.723
19	4.33	0.9299	-0.1177	3.2123	-0.2409	3.9131	0.0463	0.2563	0.6241	-0.2252	0.0991	0.411	-0.5982	-0.3153	-0.1672	0.6967	0.0465	0.0241	0.322	0.0522	0.3375	4.6614	26.824	30.7582
20	5.777	-0.5921	2.1976	3.4628	-0.0788	2.3966	-0.1796	0.3325	0.7784	-0.3222	-0.0407	-0.8699	-0.3342	0.4912	0.1705	0.8699	-0.1147	0.1561	0.4434	0.0184	0.5293	34.9257	28.5921	2.8329
21	4.2281	-0.8571	-0.2035	4.4004	-0.3115	2.8262	0.0374	0.3492	0.0382	-0.5202	-0.0232	-0.0919	-0.3101	0.1126	0.0079	0.957	-0.0476	0.124	0.3895	0.0416	0.4206	29.2675	21.8264	-1.2189
22	0.9571	-0.2838	-1.7552	1.1731	0.5873	3.0398	0.1661	-0.3276	0.1399	0.1081	0.0274	-0.1536	-0.3348	0.5141	-0.1939	0.8095	-0.1134	0.0325	0.4729	0.0339	0.4331	22.521	30.1628	20.0034
23	3.081	0.6433	-0.9892	3.8211	-1.4854	7.0191	0.1659	-0.364	0.4028	0.3286	-0.2222	-0.2905	-1.1284	1.2132	-0.0353	0.8436	-0.1757	0.0978	0.5042	0.0209	0.4328	19.3383	36.5783	27.1017

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 17 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 18 through 40 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 41 through 60 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 61 through 90 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 91 through 108 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 109 through 119 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 120 through 135 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 136 through 151 )
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 152 through 191 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 192 through 209 )
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 210 through 230 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 3 through 33 )
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 34 through 91 )
14	X-RAY DIFFRACTION	14	chain 'L' and (resid 92 through 132 )
15	X-RAY DIFFRACTION	15	chain 'L' and (resid 133 through 215 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 1 through 75 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 76 through 119 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 120 through 151 )
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 152 through 230 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 3 through 33 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 34 through 91 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 92 through 132 )
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 133 through 215 )

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