PDB-5tgb: Structure of chimeric 02-CB Fab, a VRC01-like germline antibody

ID or keywords:

Entry

Database: PDB / ID: 5tgb

Title

Structure of chimeric 02-CB Fab, a VRC01-like germline antibody

Components

02-CB Fab Heavy Chain
02-CB Fab Light Chain

Keywords

IMMUNE SYSTEM / Fab / germline / VRC01-like / CD4-BS / HIV-1 / CDRH3

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.741 Å

Authors

Pancera, M.

Funding support

United States, 1items

Citation

Journal: Cell Rep / Year: 2016
Title: Differences in Allelic Frequency and CDRH3 Region Limit the Engagement of HIV Env Immunogens by Putative VRC01 Neutralizing Antibody Precursors.
Authors: Yacoob, C. / Pancera, M. / Vigdorovich, V. / Oliver, B.G. / Glenn, J.A. / Feng, J. / Sather, D.N. / McGuire, A.T. / Stamatatos, L.

History

Deposition	Sep 27, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Apr 18, 2018	Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Oct 16, 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	5tgb.cif.gz	471 KB	Display	PDBx/mmCIF format
PDB format	pdb5tgb.ent.gz	398.8 KB	Display	PDB format
PDBx/mmJSON format	5tgb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5tgb_validation.pdf.gz	452.6 KB	Display	wwPDB validaton report
Full document	5tgb_full_validation.pdf.gz	460.6 KB	Display
Data in XML	5tgb_validation.xml.gz	29 KB	Display
Data in CIF	5tgb_validation.cif.gz	39.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tg/5tgb ftp://data.pdbj.org/pub/pdb/validation_reports/tg/5tgb	HTTPS FTP

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Related structure data

Related structure data	5tf1C 5tfsC 5tes C: citing same article (ref.)
Similar structure data	2ajz-1 6wiy-d 3w9d-2 5bk5-4 4yhl-d 6wju-2 2orb-2 6ubi-1 5wuv-d 4jfx-1 5ggu-2 1hq4-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#163 - Jul 2013 HIV Capsid similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

H: 02-CB Fab Heavy Chain

L: 02-CB Fab Light Chain

A: 02-CB Fab Heavy Chain

B: 02-CB Fab Light Chain

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

1

H: 02-CB Fab Heavy Chain

L: 02-CB Fab Light Chain

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

2

A: 02-CB Fab Heavy Chain

B: 02-CB Fab Light Chain

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

Unit cell

Length a, b, c (Å)	199.793, 64.638, 81.278
Angle α, β, γ (deg.)	90.00, 101.49, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Antibody	02-CB Fab Heavy Chain Mass: 23970.787 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody	02-CB Fab Light Chain Mass: 23019.514 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.74 Å³/Da / Density % sol: 55.05 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% isopropanol, 20% PEG 4000, 0.1 M Sodium citrate pH 5.6

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.741→47.213 Å / Num. obs: 25516 / % possible obs: 95 % / Redundancy: 3.5 % / Net I/σ(I): 4.8

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Processing

Software

Name	Version	Classification
PHENIX	1.10.1_2155	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Resolution: 2.741→47.213 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.17 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2856	1284	5.06 %
R_work	0.2486	-	-
obs	0.2505	25389	94.05 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.741→47.213 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6475	0	0	18	6493

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6641
X-RAY DIFFRACTION	f_angle_d	0.58	9038
X-RAY DIFFRACTION	f_dihedral_angle_d	12.366	3946
X-RAY DIFFRACTION	f_chiral_restr	0.043	1000
X-RAY DIFFRACTION	f_plane_restr	0.004	1152

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 (%)
2.741-2.8507	0.4013	77	0.3515	1800	X-RAY DIFFRACTION	63
2.8507-2.9804	0.3346	131	0.3241	2483	X-RAY DIFFRACTION	88
2.9804-3.1375	0.3091	149	0.3211	2824	X-RAY DIFFRACTION	100
3.1375-3.334	0.3579	158	0.2956	2807	X-RAY DIFFRACTION	100
3.334-3.5914	0.3175	164	0.2798	2821	X-RAY DIFFRACTION	100
3.5914-3.9526	0.3648	148	0.3366	2693	X-RAY DIFFRACTION	96
3.9526-4.5242	0.2737	142	0.2027	2881	X-RAY DIFFRACTION	100
4.5242-5.6985	0.1996	147	0.1881	2868	X-RAY DIFFRACTION	100
5.6985-47.2205	0.2473	168	0.2105	2928	X-RAY DIFFRACTION	100

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	4.4168	-1.1059	-1.0488	1.5063	0.2027	3.5405	-0.1646	-0.2325	-0.7984	0.5928	-0.1629	0.7757	0.6426	-0.186	0.3915	0.8613	-0.0369	0.2162	0.3258	-0.0263	0.6832	212.4774	-42.5562	32.0445
2	8.6051	0.4839	3.3287	2.649	4.2876	6.8575	-0.5599	0.3017	1.0427	0.0121	0.6258	0.0177	-0.4441	0.0186	0.1446	0.5555	0.0016	0.1595	0.3196	-0.104	0.8423	212.7513	-33.1493	24.3908
3	2.8856	2.7458	1.2904	3.593	0.2494	2.3664	0.5025	0.9477	-0.6969	0.5264	0.0004	2.3859	0.2144	0.005	-0.4102	0.6176	0.0395	0.1641	0.3789	-0.2092	1.2093	208.6478	-44.1347	20.3792
4	4.0629	1.071	0.9622	3.2457	0.4289	0.9498	-0.0783	-0.2572	-0.0749	0.4658	-0.096	0.0034	-0.0359	-0.1766	0.1321	0.6592	0.1217	0.1263	0.3613	-0.0249	0.4244	220.2351	-28.3107	32.6611
5	6.0005	0.0479	-1.2538	5.5879	1.2714	3.8026	-0.4871	-1.6753	0.4388	2.1586	0.4653	-1.0055	0.2265	-0.3374	0.017	1.0968	0.3228	-0.0456	0.9122	-0.001	0.5642	230.9193	-18.0885	48.8484
6	3.2211	-1.5317	-0.7959	4.6636	2.2692	6.1439	-0.4618	0.4312	0.8164	-0.2527	0.1388	1.697	-0.5409	-0.24	0.289	0.5046	0.0354	-0.01	0.5105	0.0812	1.0611	198.9755	-20.109	17.8452
7	9.2378	0.5238	2.5644	2.5313	-0.1628	2.1969	0.0786	-1.113	-0.0074	0.4156	-0.1524	0.7091	0.1012	-0.5252	-0.0293	0.7154	-0.0509	0.3141	0.4528	-0.1304	0.8392	197.2721	-27.1188	29.104
8	2.5857	-0.2797	0.1383	6.7161	-4.3029	8.1492	0.9545	0.8087	-0.4843	0.2849	0.8242	0.7113	-0.5723	-0.0545	-1.829	0.6139	0.1958	0.1137	0.7729	-0.1598	1.307	192.7814	-21.9677	19.26
9	3.7572	-2.3499	-1.6033	5.0499	5.8929	8.2513	0.4848	0.2996	0.5021	0.0188	-0.5532	-0.453	-0.3395	-0.9766	0.2462	0.6302	0.0808	0.1886	0.5194	-0.0023	0.8198	200.74	-23.5816	25.3763
10	0.3756	-2.1703	-1.1142	9.8163	4.8552	1.9663	0.7417	0.4358	1.1369	0.8498	-0.0005	-0.9359	0.5771	-0.4801	-0.1533	0.642	0.0238	0.1199	0.4788	-0.0851	0.9335	205.3604	-14.7304	25.6245
11	7.909	-0.2415	-0.1134	2.4555	0.4149	0.4394	0.3809	-0.3554	0.4809	0.4611	-0.1665	-0.2622	-0.0683	0.0482	-0.2776	0.7169	0.0224	-0.0166	0.3193	-0.0915	0.6525	226.1109	-5.222	35.2846
12	0.2476	0.7374	-1.0195	4.7847	-3.5238	4.5419	0.1727	-0.0393	-0.3438	0.6918	-0.0216	-0.4687	-0.9433	0.4509	-0.1965	0.6	0.029	-0.0085	0.4825	-0.1207	0.6897	232.3434	-0.1013	24.1392
13	2.1138	-4.3108	-6.4968	1.4959	2.409	3.7017	0.0871	0.3479	-0.8236	0.5456	-0.0435	0.4254	-0.1109	-0.4002	0.0767	0.716	0.0372	0.0051	0.5606	-0.0085	0.7347	220.0307	-11.7481	31.303
14	2.0689	-0.6876	0.5754	1.5625	-0.7488	1.1158	-0.1546	-0.0222	-0.0168	0.3871	0.0905	0.2996	-0.1792	-0.0197	0.0139	0.6516	-0.0057	0.0354	0.3087	-0.1127	0.6975	228.5803	-1.8771	30.9632
15	4.7292	1.8867	3.5461	6.0762	-0.4343	3.4046	0.707	0.3782	-1.3594	-0.9015	-0.2797	0.0452	1.2025	1.0413	-0.4075	0.7668	0.3866	-0.3365	0.8917	-0.4265	1.088	125.5023	-28.7436	-20.1124
16	0.8643	-1.2043	-0.6476	3.4904	-0.5311	3.0384	0.7458	1.1743	-0.622	-0.6758	-0.4225	0.8747	0.726	0.5603	-0.2288	0.7057	0.2252	-0.3432	0.7435	-0.3471	0.7084	116.5345	-21.1971	-21.573
17	2.4093	-1.6322	1.7335	3.3192	-3.7239	3.3024	0.5544	1.0053	-0.3053	-0.6777	-0.4757	0.3131	0.6072	0.8991	-0.0537	0.7427	0.2923	-0.2005	0.8663	-0.3226	0.5902	122.9329	-21.7043	-20.4707
18	2.5342	-2.1128	-0.0424	3.939	-0.7679	2.4602	0.0246	0.5307	-0.172	-0.0326	-0.5885	-0.0697	0.2467	0.1021	0.5201	0.3375	0.0645	-0.0578	1.0217	-0.1609	0.7025	141.3541	-35.1291	2.0499
19	4.1289	-1.5542	0.4738	4.1274	-1.5994	2.8692	0.6012	0.6126	-0.607	-0.2851	-0.6621	-0.0035	0.2593	0.1038	0.1754	0.364	0.1107	-0.0894	0.9334	-0.1755	0.7197	142.3871	-41.1141	1.2945
20	2.5939	-0.0855	-0.323	4.7322	-4.0252	7.291	0.1425	0.1273	-0.0796	0.5134	0.1367	0.4536	-0.8883	0.4081	-0.1437	0.4637	-0.0147	0.1101	0.4195	-0.2909	0.64	117.5856	-12.3899	4.3778
21	4.2552	0.6379	0.0442	2.0036	-1.1242	6.1704	0.2018	0.0181	0.2403	-0.0684	0.1182	0.7448	-0.2258	-0.2888	-0.3523	0.3351	0.0303	-0.0875	0.4049	-0.1741	1.0022	109.5828	-15.6953	-2.1736
22	1.3646	-1.4911	0.7785	1.609	-1.2322	3.8414	0.4295	0.0403	-0.264	-0.168	0.1923	0.2631	0.0755	0.2327	-0.5432	0.4111	-0.0451	-0.0028	0.3214	-0.168	0.6638	114.4542	-18.1463	-1.3722
23	2.4078	0.3707	0.2933	0.7734	-1.7332	1.9959	0.1552	0.0984	-0.4253	0.0044	-0.4009	-0.2642	-0.1957	0.656	0.2846	0.3895	-0.0967	-0.0511	0.6221	-0.1425	0.6422	139.4433	-26.2436	8.5781
24	7.1761	4.2384	-1.7233	4.8104	2.1152	4.9265	0.2127	-0.1434	-0.8501	1.0103	-0.3512	-0.2932	-1.4284	1.1124	0.2101	0.6114	-0.1411	-0.1501	1.0271	0.1598	0.6524	152.1555	-17.3689	9.4435
25	4.272	-1.417	-1.253	2.8528	-0.5559	2.4956	0.2514	0.4785	-0.2793	0.4124	-0.3942	-0.321	-0.1582	0.838	0.1223	0.4426	-0.1322	-0.1469	0.8138	0.0309	0.5924	144.8654	-24.0613	9.008

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 33 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 34 through 44 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 45 through 60 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 61 through 190 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 191 through 213 )
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 2 through 33 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 34 through 61 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 62 through 75 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 76 through 98 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 99 through 109 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 110 through 146 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 147 through 159 )
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 160 through 170 )
14	X-RAY DIFFRACTION	14	chain 'L' and (resid 171 through 209 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 1 through 16 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 17 through 60 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 61 through 119 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 120 through 173 )
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 174 through 215 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 1 through 18 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 19 through 75 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 76 through 98 )
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 99 through 146 )
24	X-RAY DIFFRACTION	24	chain 'B' and (resid 147 through 159 )
25	X-RAY DIFFRACTION	25	chain 'B' and (resid 160 through 207 )

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