PDB-6cjk: Anti HIV Fab 10A

ID or keywords:

Entry

Database: PDB / ID: 6cjk

Title

Anti HIV Fab 10A

Components

Immunoglobulin Fab heavy chain
Immunoglobulin Fab light chain

Keywords

IMMUNE SYSTEM /

Fab /

HIV

Function / homology

Immunoglobulins /

Immunoglobulin-like /

Sandwich / Mainly Beta /

ACETATE ION

Function and homology information

Biological species

Oryctolagus cuniculus (rabbit)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.795 Å

Authors

Hangartner, L. / Ward, A.B. / Wilson, I.A. / Oyen, D.

Funding support

United States, 2items

Organization	Grant number	Country
International AIDS Vaccine Initiative	IAVI SFP 2120/2121
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	UM1AI100663	United States

Citation

Journal: Immunity / Year: 2018
Title: Electron-Microscopy-Based Epitope Mapping Defines Specificities of Polyclonal Antibodies Elicited during HIV-1 BG505 Envelope Trimer Immunization.
Authors: Matteo Bianchi / Hannah L Turner / Bartek Nogal / Christopher A Cottrell / David Oyen / Matthias Pauthner / Raiza Bastidas / Rebecca Nedellec / Laura E McCoy / Ian A Wilson / Dennis R Burton ...
Abstract: Characterizing polyclonal antibody responses via currently available methods is inherently complex and difficult. Mapping epitopes in an immune response is typically incomplete, which creates a ...

History

Deposition	Feb 26, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 15, 2018	Provider: repository / Type: Initial release
Revision 1.1	Aug 29, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0	Dec 18, 2019	Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6cjk.cif.gz	473.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6cjk.ent.gz	411.1 KB	Display	PDB format
PDBx/mmJSON format	6cjk.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/cj/6cjk ftp://data.pdbj.org/pub/pdb/validation_reports/cj/6cjk	HTTPS FTP

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Related structure data

Related structure data	7552C 7553C 7554C 7555C 7556C 7557C 7570C 7887C 7888C 7889C 7890C 7891C 7892C 7893C 7894C 7895C 7896C 7903C 7904C 7906C 6didC C: citing same article (ref.)
Similar structure data	5ds8-1 6z3k-9 5fgb-2 4r7d-1 2v7h-1 3uyr-d 4kaq-d 6ldv-d 6lkt-d 4jo2-2 1kfa-2 2uyl-1 7kqy-1 4kk5-3 4qhk-3 4dn3-d 1mfb-d 2uyl-2 6xrj-4 1rzi-8 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

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	#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

A: Immunoglobulin Fab light chain

B: Immunoglobulin Fab heavy chain

C: Immunoglobulin Fab light chain

D: Immunoglobulin Fab heavy chain

hetero molecules

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

1

A: Immunoglobulin Fab light chain

B: Immunoglobulin Fab heavy chain

hetero molecules

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

2

C: Immunoglobulin Fab light chain

D: Immunoglobulin Fab heavy chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	51.173, 63.558, 72.649
Angle α, β, γ (deg.)	67.99, 87.87, 76.73
Int Tables number	1
Space group name H-M	P1

#1: Antibody	Immunoglobulin Fab light chain Mass: 23047.424 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#2: Antibody	Immunoglobulin Fab heavy chain Mass: 23366.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 547 / 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: 2.29 Å³/Da / Density % sol: 46.37 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium citrate pH 5.26, 0.17 M ammonium acetate, 15% glycerol, 19% PEG4000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03315 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03315 Å / Relative weight: 1
Reflection	Resolution: 1.795→40.703 Å / Num. obs: 73928 / % possible obs: 96.3 % / Redundancy: 3.2 % / CC_1/2: 0.856 / R_pim(I) all: 0.048 / R_sym value: 0.074 / Net I/σ(I): 16.5
Reflection shell	Resolution: 1.8→1.83 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.12_2829	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Resolution: 1.795→40.703 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.3 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2056	3841	5.2 %
R_work	0.1633	-	-
obs	0.1656	73915	95.87 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.795→40.703 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6242	0	18	547	6807

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	6616
X-RAY DIFFRACTION	f_angle_d	1.073	9106
X-RAY DIFFRACTION	f_dihedral_angle_d	18.941	2331
X-RAY DIFFRACTION	f_chiral_restr	0.169	1067
X-RAY DIFFRACTION	f_plane_restr	0.007	1169

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 (%)
1.795-1.8177	0.372	107	0.3618	2155	X-RAY DIFFRACTION	78
1.8177-1.8416	0.3991	113	0.3329	2405	X-RAY DIFFRACTION	90
1.8416-1.8668	0.3273	118	0.3012	2516	X-RAY DIFFRACTION	92
1.8668-1.8935	0.281	110	0.2766	2619	X-RAY DIFFRACTION	94
1.8935-1.9218	0.3252	156	0.2608	2537	X-RAY DIFFRACTION	95
1.9218-1.9518	0.2858	154	0.2326	2564	X-RAY DIFFRACTION	95
1.9518-1.9838	0.2885	136	0.2158	2621	X-RAY DIFFRACTION	96
1.9838-2.018	0.2106	127	0.2001	2583	X-RAY DIFFRACTION	95
2.018-2.0547	0.2003	144	0.1942	2650	X-RAY DIFFRACTION	96
2.0547-2.0942	0.2485	121	0.1854	2541	X-RAY DIFFRACTION	96
2.0942-2.137	0.2296	137	0.1938	2683	X-RAY DIFFRACTION	97
2.137-2.1834	0.2338	136	0.186	2599	X-RAY DIFFRACTION	96
2.1834-2.2342	0.2127	121	0.1789	2634	X-RAY DIFFRACTION	97
2.2342-2.2901	0.2392	127	0.1723	2583	X-RAY DIFFRACTION	96
2.2901-2.352	0.2066	149	0.1664	2635	X-RAY DIFFRACTION	97
2.352-2.4212	0.2287	155	0.1699	2633	X-RAY DIFFRACTION	97
2.4212-2.4993	0.2581	145	0.1726	2606	X-RAY DIFFRACTION	97
2.4993-2.5886	0.2044	162	0.1655	2607	X-RAY DIFFRACTION	97
2.5886-2.6923	0.207	177	0.1566	2622	X-RAY DIFFRACTION	97
2.6923-2.8148	0.2084	156	0.1502	2648	X-RAY DIFFRACTION	98
2.8148-2.9631	0.2038	132	0.1521	2626	X-RAY DIFFRACTION	98
2.9631-3.1487	0.1812	181	0.1437	2675	X-RAY DIFFRACTION	98
3.1487-3.3917	0.1805	165	0.1377	2617	X-RAY DIFFRACTION	99
3.3917-3.7328	0.1687	162	0.1351	2665	X-RAY DIFFRACTION	99
3.7328-4.2725	0.1776	122	0.1261	2730	X-RAY DIFFRACTION	99
4.2725-5.3809	0.1678	166	0.1225	2636	X-RAY DIFFRACTION	99
5.3809-40.7138	0.2104	162	0.1862	2684	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	4.7346	4.1454	-2.8961	5.3194	-2.333	2.9983	0.0545	-0.3572	0.0913	0.255	-0.0684	0.0369	-0.0408	-0.063	-0.0386	0.2598	0.0311	-0.0789	0.3489	-0.028	0.2704	17.7534	4.124	16.9743
2	4.0181	0.254	1.8447	1.5604	-0.2256	3.784	0.1158	-0.2339	-0.2497	0.124	0.0185	-0.1015	0.2022	-0.2742	-0.1592	0.1706	0.0109	-0.0001	0.2763	-0.0023	0.2298	19.6622	-6.2058	14.3999
3	1.5319	0.6635	-0.1679	2.2582	-0.3598	0.9319	-0.0573	-0.0148	0.0542	-0.1037	-0.0015	-0.137	-0.0107	0.051	0.0658	0.1646	0.0098	0.0069	0.224	-0.0071	0.2259	22.2904	-0.6825	6.7126
4	1.3394	-0.984	0.4525	2.5744	0.0166	0.6366	-0.0233	-0.0711	0.1422	0.1834	0.0483	-0.087	-0.024	-0.0248	-0.0402	0.1504	0.0026	0.0617	0.2434	-0.0127	0.197	8.4554	6.8662	8.137
5	5.7698	-1.7624	0.4556	2.1573	-0.2973	0.9758	-0.3331	-0.7437	0.5261	0.2316	0.2943	-0.1138	-0.0719	-0.1904	0.08	0.2449	0.0348	0.0072	0.2905	-0.0808	0.3144	1.5832	26.7999	8.2042
6	3.3093	-1.6262	0.8791	1.6823	-0.4419	1.1884	-0.0372	-0.3433	-0.1299	0.2485	0.0909	0.2163	-0.1417	-0.2522	-0.0314	0.2467	0.0063	0.0428	0.2457	0.0097	0.2926	-1.2639	24.3775	8.4118
7	5.4998	-4.7362	1.9661	4.2381	-1.7374	0.7216	-0.1946	-0.2253	0.686	0.2144	0.3741	-0.4075	-0.0693	0.0975	-0.1571	0.3732	0.0717	-0.0052	0.4146	-0.1641	0.5237	-2.3936	34.1485	10.5107
8	4.6458	2.5837	-2.5114	4.6304	1.1598	4.9191	-0.2308	0.6739	1.254	-0.014	0.5122	-0.3172	-0.3733	0.197	-0.27	0.4279	0.0386	0.0737	0.3052	-0.0267	0.499	-1.9095	37.0498	6.0319
9	0.5596	0.2325	0.104	1.1965	-0.2396	0.5841	-0.0232	0.0417	-0.0047	-0.0278	0.0858	-0.0285	0.0128	0.0021	-0.0668	0.1835	-0.0041	0.0177	0.2312	-0.0125	0.2006	-0.2903	-3.2272	0.973
10	2.1054	0.3171	2.6178	4.199	0.6456	3.4142	0.0803	-0.2985	-0.1153	0.2516	-0.2255	-0.0587	-0.0571	0.095	0.1534	0.2095	0.015	-0.0191	0.1266	-0.0408	0.2719	-1.1356	16.5172	-0.125
11	4.5621	3.8486	-1.4816	3.5449	-1.8267	2.5744	-0.1375	0.2944	0.242	-0.2173	0.3021	0.2779	-0.1378	0.0709	-0.112	0.2101	0.0082	0.0279	0.2223	0.0156	0.2734	-3.6671	20.2217	-10.002
12	4.1507	-0.3789	3.1205	1.6393	-0.5645	2.419	-0.2444	0.7999	0.4188	-0.4964	0.0018	-0.1155	-0.6723	0.6405	0.2654	0.5085	-0.1172	0.0147	0.3545	0.0663	0.2845	4.8359	8.9313	35.8289
13	3.8943	0.2627	0.6745	2.3796	-0.0317	4.4046	-0.2964	0.0465	0.3349	-0.2393	0.1253	0.1423	-0.5973	-0.2175	0.1271	0.2859	-0.0167	-0.059	0.1935	-0.0132	0.1914	-5.9062	5.6348	37.4424
14	2.6402	0.4976	1.9421	0.7216	0.4848	3.2027	-0.4066	0.0728	0.4727	-0.1082	0.0521	0.2168	-0.8592	-0.035	0.3152	0.3888	0.0193	-0.0565	0.1932	-0.0124	0.2514	-5.1917	9.9046	38.9529
15	1.7877	-1.248	0.4138	2.2049	-0.1596	0.7613	0.0451	0.171	-0.1577	-0.0197	-0.022	-0.0969	0.2412	0.226	-0.0035	0.2972	0.0079	0.021	0.2719	-0.0322	0.2328	13.9664	-15.4798	43.9713
16	3.7093	-2.8561	-4.5899	7.933	6.2466	6.9402	0.191	1.1706	-0.6113	-0.6498	0.0131	-0.2898	0.3131	0.1037	-0.1057	0.489	0.1185	-0.0684	0.5741	-0.2188	0.4128	17.9614	-29.9465	37.4901
17	2.8419	0.5625	0.7103	3.8346	4.7292	5.869	-0.1917	0.5157	-0.1898	-0.1363	0.284	-0.5718	0.2043	0.5202	-0.1076	0.2686	0.0434	0.0529	0.386	0.0167	0.3931	25.428	-23.1815	44.915
18	5.318	3.1289	1.9354	3.6973	4.2587	5.9799	0.3858	0.2283	-0.8657	0.7062	-0.2757	-0.4562	1.1101	0.366	-0.0044	0.4092	0.0961	-0.0064	0.2737	0.0177	0.4525	23.9426	-28.6214	49.0454
19	1.7689	-0.3645	0.4657	1.7469	-0.0024	2.3009	-0.1141	-0.3528	-0.112	0.1451	0.0698	0.2973	0.0152	-0.4681	0.0766	0.2201	-0.0074	0.0021	0.3478	0.0389	0.1982	-17.6087	-8.3954	31.3476
20	2.4298	0.9039	2.3573	1.6966	-0.6201	3.8783	0.0353	0.0415	0.0342	-0.035	-0.0505	0.0333	-0.2603	-0.1595	0.01	0.2441	0.0165	-0.0065	0.2478	-0.005	0.2081	-14.8734	-0.178	26.7303
21	1.6034	-0.2194	0.6162	0.6466	0.2725	1.2265	-0.0099	-0.1397	0.0597	0.1085	-0.018	0.0682	-0.0308	-0.2563	0.0262	0.2443	0.0097	0.0074	0.33	0.0099	0.2136	-14.916	-5.7484	27.9013
22	3.1453	-2.1677	0.4453	5.6341	-5.0624	5.5499	0.3993	0.0842	-0.4531	-0.4353	-0.2487	0.2038	1.1005	-0.3008	-0.161	0.397	-0.0618	-0.0815	0.2713	-0.0034	0.2691	-4.8759	-23.4588	28.1134
23	3.5238	-1.0867	-1.9164	5.5612	1.5963	3.7719	0.1167	-0.5409	-0.2375	0.193	0.2544	-0.2917	1.0099	1.1413	-0.4336	0.3856	0.1136	-0.0472	0.405	-0.0136	0.2761	12.7937	-32.1431	52.5691
24	1.7059	-0.643	0.5593	1.9934	-0.4317	6.1308	0.0469	-0.1082	-0.0547	-0.0244	0.0482	0.1863	0.6767	0.0073	-0.0968	0.3455	-0.0759	-0.0222	0.234	0.022	0.259	0.6175	-24.9341	44.4073
25	3.3706	1.6747	0.6377	3.4949	-0.9822	0.743	-0.0886	0.0923	0.2606	-0.2592	0.0999	0.133	0.2423	0.1724	0.0975	0.2929	-0.0094	-0.048	0.2265	-0.0157	0.2979	3.8404	-20.3717	41.5924
26	1.9715	0.384	2.2129	0.7575	0.0572	5.8771	-0.0157	-0.1801	0.0417	-0.2382	-0.0799	0.1266	0.2233	-0.3015	0.1008	0.3264	-0.0021	-0.0404	0.2465	-0.0079	0.2797	1.1921	-26.7293	49.3364
27	1.8271	-2.3954	1.4692	3.6696	-2.1886	1.9548	-0.4136	-0.024	-0.2589	0.1622	0.1934	0.17	-0.0255	0.0392	0.1762	0.5614	-0.1067	-0.0842	0.2961	0.0466	0.4047	-1.9668	-32.6609	47.2047

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 2:17 )	A	2 - 17
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 18:38 )	A	18 - 38
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 39:83 )	A	39 - 83
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 84:128 )	A	84 - 128
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 129:149 )	A	129 - 149
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 150:187 )	A	150 - 187
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 188:197 )	A	188 - 197
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 198:211 )	A	198 - 211
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 4:157 )	B	4 - 157
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 158:175 )	B	158 - 175
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 176:211 )	B	176 - 211
12	X-RAY DIFFRACTION	12	( CHAIN C AND RESID 1:25 )	C	1 - 25
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 26:48 )	C	26 - 48
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 49:95 )	C	49 - 95
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 96:173 )	C	96 - 173
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 174:186 )	C	174 - 186
17	X-RAY DIFFRACTION	17	( CHAIN C AND RESID 187:199 )	C	187 - 199
18	X-RAY DIFFRACTION	18	( CHAIN C AND RESID 200:211 )	C	200 - 211
19	X-RAY DIFFRACTION	19	( CHAIN D AND RESID 4:39 )	D	4 - 39
20	X-RAY DIFFRACTION	20	( CHAIN D AND RESID 40:59 )	D	40 - 59
21	X-RAY DIFFRACTION	21	( CHAIN D AND RESID 60:106 )	D	60 - 106
22	X-RAY DIFFRACTION	22	( CHAIN D AND RESID 107:119 )	D	107 - 119
23	X-RAY DIFFRACTION	23	( CHAIN D AND RESID 120:134 )	D	120 - 134
24	X-RAY DIFFRACTION	24	( CHAIN D AND RESID 135:157 )	D	135 - 157
25	X-RAY DIFFRACTION	25	( CHAIN D AND RESID 158:175 )	D	158 - 175
26	X-RAY DIFFRACTION	26	( CHAIN D AND RESID 176:200 )	D	176 - 200
27	X-RAY DIFFRACTION	27	( CHAIN D AND RESID 201:210 )	D	201 - 210

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