PDB-6qna: Structure of bovine anti-RSV hybrid Fab B13HC-B4LC

ID or keywords:

Entry

Database: PDB / ID: 6qna

Title

Structure of bovine anti-RSV hybrid Fab B13HC-B4LC

Components

B13 Heavy chain
B4 light chain

Keywords

IMMUNE SYSTEM / cattle antibodies / bovine respiratory syncytial virus / anti-RSV B4 / anti-RSV B13 / 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: 2.62 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	Jan 24, 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 1.3	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6qna.cif.gz	671.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6qna.ent.gz	564.8 KB	Display	PDB format
PDBx/mmJSON format	6qna.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6qna_validation.pdf.gz	498.5 KB	Display	wwPDB validaton report
Full document	6qna_full_validation.pdf.gz	510.6 KB	Display
Data in XML	6qna_validation.xml.gz	57.5 KB	Display
Data in CIF	6qna_validation.cif.gz	78.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qn/6qna ftp://data.pdbj.org/pub/pdb/validation_reports/qn/6qna	HTTPS FTP

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Related structure data

Related structure data	6qn7C 6qn8C 6qn9SC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1i9i-d 5mv3-2 2r23-d 3mly-2 3bpc-d 1q9l-1 2gsi-1 1q9k-d 5ihz-4 3t77-d 5ea0-d 5mu2-7 5mv3-3 4tuo-2 5f89-1 2dtm-d 5vkk-2 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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

6qn7C

6qn8C

6qn9SC

C: citing same article (ref.)

S: Starting model for refinement

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: B13 Heavy chain

L: B4 light chain

A: B13 Heavy chain

B: B4 light chain

C: B13 Heavy chain

D: B4 light chain

E: B13 Heavy chain

F: B4 light chain

hetero molecules

194 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

H: B13 Heavy chain

L: B4 light chain

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

2

A: B13 Heavy chain

B: B4 light chain

hetero molecules

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

3

C: B13 Heavy chain

D: B4 light chain

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

4

E: B13 Heavy chain

F: B4 light chain

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

Unit cell

Length a, b, c (Å)	43.440, 76.270, 130.030
Angle α, β, γ (deg.)	89.66, 87.35, 88.60
Int Tables number	1
Space group name H-M	P1

#1: Antibody	B13 Heavy chain Mass: 25837.941 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Homo sapiens (human)
#2: Antibody	B4 light chain Mass: 22676.014 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.22 Å³/Da / Density % sol: 44.52 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 28.0% w/v Polyethylene Glycol Monomethyl Ether 2000 0.1 M bis-Tris

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 9, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 2.62→65.9 Å / Num. obs: 49218 / % possible obs: 98.2 % / Redundancy: 3.5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.05 / Net I/σ(I): 13.8
Reflection shell	Resolution: 2.62→2.67 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.931 / Num. unique obs: 2446 / CC_1/2: 0.521 / % possible all: 98.1

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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
Starting model: 6QN9

6qn9

Resolution: 2.62→65.617 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30.07

	R_factor	Num. reflection	% reflection
R_free	0.2499	2230	4.53 %
R_work	0.2201	-	-
obs	0.2214	49210	98.22 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.62→65.617 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13082	0	6	51	13139

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	13371
X-RAY DIFFRACTION	f_angle_d	0.547	18235
X-RAY DIFFRACTION	f_dihedral_angle_d	14.234	8008
X-RAY DIFFRACTION	f_chiral_restr	0.042	2148
X-RAY DIFFRACTION	f_plane_restr	0.004	2292

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 (%)
2.62-2.677	0.3758	164	0.3546	2906	X-RAY DIFFRACTION	98
2.677-2.7393	0.4151	171	0.3373	2886	X-RAY DIFFRACTION	98
2.7393-2.8078	0.3404	149	0.321	2922	X-RAY DIFFRACTION	98
2.8078-2.8837	0.3355	151	0.3035	2956	X-RAY DIFFRACTION	98
2.8837-2.9686	0.3497	127	0.2908	2901	X-RAY DIFFRACTION	98
2.9686-3.0644	0.3461	132	0.297	2976	X-RAY DIFFRACTION	98
3.0644-3.1739	0.3368	129	0.2846	2952	X-RAY DIFFRACTION	98
3.1739-3.301	0.2667	117	0.2711	2991	X-RAY DIFFRACTION	99
3.301-3.4512	0.34	118	0.2712	2917	X-RAY DIFFRACTION	98
3.4512-3.6331	0.2921	130	0.2559	3005	X-RAY DIFFRACTION	98
3.6331-3.8607	0.2989	103	0.2532	2916	X-RAY DIFFRACTION	98
3.8607-4.1588	0.2616	127	0.2192	2949	X-RAY DIFFRACTION	99
4.1588-4.5772	0.2098	163	0.1788	2936	X-RAY DIFFRACTION	99
4.5772-5.2393	0.1832	164	0.1654	2917	X-RAY DIFFRACTION	98
5.2393-6.6	0.2266	133	0.1881	2964	X-RAY DIFFRACTION	99
6.6-65.6374	0.1944	152	0.1775	2886	X-RAY DIFFRACTION	97

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	6.8321	-2.6479	-3.0281	4.5828	0.7886	4.8033	-0.0103	-0.3886	0.4355	0.0115	0.0717	-0.5051	0.0594	0.2872	0.0131	0.456	-0.0374	-0.0643	0.4731	0.0426	0.6004	13.2934	80.7118	58.6054
2	5.9645	-0.8957	0.9863	7.7313	0.4276	6.033	0.4261	-0.6496	-0.3332	0.7614	0.0813	-0.4887	0.3281	-0.1824	-0.3893	0.6716	-0.0406	-0.0042	0.6748	0.1143	0.7692	-2.1889	68.3686	86.0207
3	5.4293	1.0614	-1.6022	7.6836	0.3676	4.5254	0.0524	0.0602	-0.4198	-0.156	-0.1507	0.01	0.7258	0.1393	0.0197	0.7984	0.1408	0.0507	0.4244	0.0336	0.6661	17.0725	59.9392	54.5628
4	4.8174	0.2939	-4.9831	2.052	-1.1319	8.6109	-0.2121	-0.0562	-0.4694	-0.1599	0.0102	0.2199	0.5971	-0.5348	0.2859	0.3546	-0.09	-0.0295	0.565	0.0122	0.6552	0.2386	62.126	69.7938
5	3.1524	0.3333	1.4491	10.1015	-0.7185	3.5776	-0.058	-0.278	-0.3401	-1.6146	0.4952	1.0092	0.2473	-0.628	-0.5323	0.9034	-0.1676	-0.0257	0.8235	0.2199	0.7897	-12.4595	57.3457	78.52
6	5.95	0.4766	-1.4253	5.5296	2.8215	5.0829	-0.4756	-1.1877	-0.8316	0.85	0.3074	0.1246	1.2489	-0.1199	-0.0306	0.8899	0.0283	0.0078	0.7735	0.0256	0.5686	-8.2355	-16.2594	-4.1478
7	3.9242	-3.5828	1.8941	4.8776	-0.1507	6.2037	0.1449	0.5982	0.1413	-0.5059	0.1662	-0.5505	0.0294	0.8074	-0.0368	0.5431	-0.024	0.0235	0.712	-0.1256	0.4813	-5.8208	-13.0729	-14.583
8	1.9145	-0.9894	1.1666	2.9065	1.1592	4.637	-0.5106	1.3773	-0.773	0.6247	0.9596	-0.6104	0.6557	0.5743	-0.4504	0.6716	-0.0069	-0.025	0.8807	-0.1638	0.535	-2.3571	-17.481	-8.1345
9	7.0157	0.2108	-0.6779	8.3536	2.0902	4.67	-0.1354	-0.1762	0.5211	-0.0387	0.0433	1.7585	-0.4206	-0.765	0.0868	0.6096	0.0448	0.0081	0.6834	-0.0811	0.9023	-17.6321	-5.4392	-12.6711
10	2.3917	0.8002	1.9647	1.5028	-0.7191	4.0553	0.5938	-0.1627	-0.2335	0.9464	0.0598	-1.0097	0.2534	0.6684	-0.4605	0.9981	0.2072	-0.2985	1.3429	-0.1129	0.684	9.2227	-4.813	15.7287
11	3.8352	1.6722	2.4456	6.3419	0.1385	2.4553	0.5793	-0.1292	-0.1843	0.777	-0.2308	-0.1457	0.1604	0.3075	-0.4176	0.9531	0.0852	-0.1038	0.9888	-0.0256	0.5235	5.0054	-1.6483	19.2801
12	4.297	0.3941	-1.54	4.1064	1.989	3.938	0.4361	-0.3376	0.2546	0.6041	0.5735	-0.5237	-0.2743	0.6483	-0.7152	1.7781	-0.0358	-0.3345	1.4077	0.0365	0.755	10.9928	-3.4564	29.2942
13	5.9117	-0.3354	1.9822	6.4889	0.7984	3.3729	0.1117	0.6073	0.615	-0.6754	0.0163	-0.0516	-0.7682	0.1597	-0.0352	1.2116	-0.1081	0.0878	0.7814	0.1621	0.7889	-7.9607	10.5923	-16.943
14	5.4113	1.6899	0.9562	8.2357	1.1672	3.0848	-0.2138	-0.4712	1.5956	-0.3106	-0.1233	1.3562	-0.822	-0.6079	-0.1085	0.768	0.0934	-0.0645	0.736	-0.0923	1.1807	-15.9079	5.0452	-8.7346
15	5.9338	-1.2997	2.437	4.5467	-0.603	5.3867	0.5512	0.0695	1.0411	-0.6147	-0.2219	0.3703	-1.2137	-0.2688	0.0088	1.107	0.0464	0.0545	0.7071	0.0786	1.0326	-11.8955	11.0307	-11.3742
16	3.9281	-1.1122	1.4543	2.7444	-2.6325	2.498	-0.2997	0.0038	0.6277	-1.2602	0.0592	0.2134	-1.2385	-0.1439	0.4089	0.753	-0.0484	0.0584	0.8365	0.0258	0.7599	-3.8479	9.1853	-7.688
17	3.3741	1.7494	1.0206	4.3735	0.3481	3.3627	0.4193	-1.6335	-0.1864	0.2566	0.1712	-0.8134	0.2336	0.2215	-0.1679	0.9037	0.0876	-0.1213	1.3769	-0.0591	0.439	16.344	3.0304	18.5209
18	4.8356	1.7682	0.8876	3.224	-0.4924	2.0608	-0.0825	0.2538	-1.1076	-0.3797	-0.0003	-0.283	-0.2746	0.8917	-0.1349	1.1891	0.0201	-0.0241	1.4483	-0.1373	0.6922	13.5273	10.0344	7.6043
19	2.3738	-0.4026	1.2562	4.4774	-0.5411	2.3995	-0.0343	0.481	0.0019	-0.6008	0.1024	-1.3468	-0.4566	1.8765	-0.3146	1.0248	-0.0982	0.0493	1.8873	-0.3361	0.8022	20.696	9.2879	15.3643
20	8.3201	3.8175	-2.0655	7.9605	-0.5645	3.8111	-0.2307	-0.3578	0.4604	0.0509	0.1163	0.6088	-0.0465	-0.432	0.0892	0.3895	0.042	-0.0444	0.5475	-0.1251	0.5532	-30.9293	41.5719	-20.427
21	4.995	2.1583	-4.516	10.0263	-5.6505	5.8629	0.4619	0.8906	-0.1176	-0.0401	-0.0175	0.7857	-0.1242	-0.1795	-0.4146	0.5701	-0.0878	-0.0156	0.6989	0.0027	0.5959	-15.8167	32.0791	-47.5261
22	7.8408	-0.0057	-0.4933	4.2719	2.0168	5.506	0.3963	-0.4305	-0.6056	0.4494	-0.1777	-0.2754	0.5738	-0.2242	-0.1682	0.7877	-0.1274	-0.0164	0.6189	0.1344	0.8068	-35.0024	20.4443	-18.5374
23	4.9232	-0.3345	-4.1878	3.8565	0.3636	4.87	-0.4734	-0.1596	-0.6264	-0.1862	-0.1422	-0.2198	0.6719	0.2095	0.47	0.5657	-0.081	-0.1806	0.6595	0.0844	0.6178	-14.5454	22.1175	-36.2361
24	4.4816	-0.6571	0.6047	8.5597	-1.0229	5.312	0.008	-0.0929	-0.3333	-0.1355	-0.4222	-1.9635	0.573	0.5413	0.4472	0.914	0.0115	0.0768	0.6893	0.1091	1.0992	-4.2954	20.2549	-42.9412
25	8.2076	3.0877	0.5173	2.7355	-0.9603	5.638	0.2488	0.0591	0.2494	0.1861	0.3087	-0.3229	0.1015	-0.1707	-0.4399	0.7534	0.1165	-0.0385	0.4648	-0.0313	0.8908	28.4802	23.4684	47.5253
26	4.2795	0.2199	0.8676	3.9334	0.2027	4.2621	-0.0893	0.4111	0.4301	0.5322	0.5138	-1.2051	-0.0061	0.4848	-0.4174	0.7338	0.1351	-0	0.5718	-0.0695	1.3182	34.2709	30.9718	45.585
27	4.4651	1.2057	0.9827	4.2857	-1.1174	3.4871	0.2346	0.5706	0.2855	-0.641	0.345	0.1553	-0.6929	0.5504	-0.4729	1.0187	-0.2121	-0.0996	1.2939	-0.0327	0.7107	14.6185	34.5567	19.0672
28	3.8742	-1.2776	-2.5494	2.0695	2.2535	3.6697	0.8801	0.2698	0.5435	-1.2212	-0.1997	-0.0846	-0.0889	0.232	-0.6091	0.9559	-0.1993	-0.092	1.3364	-0.0296	0.8045	16.7446	31.949	12.0871
29	4.7304	-0.4351	1.7961	6.0838	-2.0794	2.4554	-0.0692	0.1388	-0.3977	0.6273	0.4488	-0.6658	-0.5545	0.1027	-0.3937	0.9536	0.1208	0.0849	0.5801	-0.0655	1.2147	34.7434	46.3193	47.473
30	5.2015	1.9936	4.1143	4.725	1.9778	4.1575	-0.5203	0.2839	-0.0097	0.2204	0.4517	-0.5873	-0.6879	-0.0299	0.1466	0.7042	0.1241	0.2595	0.6378	0.0017	0.823	24.9361	45.647	37.9047
31	4.9823	1.0207	2.8177	7.3499	1.4151	6.1101	-0.5561	-0.2124	0.2199	-0.121	0.0088	0.7955	-1.1238	-0.7617	0.6556	1.0404	0.0181	-0.0581	1.1383	-0.0125	0.5579	5.942	45.9492	23.265

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 2 through 139 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 140 through 240 )
3	X-RAY DIFFRACTION	3	chain 'L' and (resid 3 through 92 )
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 93 through 130 )
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 131 through 213 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 2 through 33 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 34 through 72 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 73 through 90 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 91 through 126 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 127 through 174 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 175 through 223 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 224 through 238 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 3 through 33 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 34 through 62 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 63 through 92 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 93 through 115 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 116 through 141 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 142 through 173 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 174 through 213 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 2 through 139 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 140 through 235 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 3 through 92 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 93 through 152 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 153 through 213 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 2 through 90 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 91 through 139 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 140 through 197 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 198 through 236 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 3 through 62 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 63 through 130 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 131 through 213 )

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