PDB-6sxi: Antibody-anti-idiotype complex: AP33 Fab (hepatitis C virus E2 an...

ID or keywords:

Entry

Database: PDB / ID: 6sxi

Title

Antibody-anti-idiotype complex: AP33 Fab (hepatitis C virus E2 antibody) - B2.1A scFv (anti-idiotype)

Components

(Single chain Fv - ...) x 2
Fab heavy chainFragment antigen-binding
Fab light chainFragment antigen-binding

Keywords

IMMUNE SYSTEM / anti-idiotype /

antigen binding fragment /

single chain Fv /

complex

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.85 Å

Authors

Taylor, G.L. / Potter, J.A. / Fadda, V. / Patel, A.H. / Owsianka, A.M. / Cowtan, V.M.

Citation

Journal: NPJ Vaccines / Year: 2021
Title: Development of a structural epitope mimic: an idiotypic approach to HCV vaccine design.
Authors: Cowton, V.M. / Owsianka, A.M. / Fadda, V. / Ortega-Prieto, A.M. / Cole, S.J. / Potter, J.A. / Skelton, J.K. / Jeffrey, N. / Di Lorenzo, C. / Dorner, M. / Taylor, G.L. / Patel, A.H.

History

Deposition	Sep 26, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 7, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jan 20, 2021	Group: Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6sxi.cif.gz	276 KB	Display	PDBx/mmCIF format
PDB format	pdb6sxi.ent.gz	230.7 KB	Display	PDB format
PDBx/mmJSON format	6sxi.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/sx/6sxi ftp://data.pdbj.org/pub/pdb/validation_reports/sx/6sxi	HTTPS FTP

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Related structure data

Similar structure data	5ukr-d 5th9-2 3b2u-2 3p5r-1 4lvh-4 3b2u-3 6b3s-1 3b2u-8 5czx-1 6h2y-d 3p5p-d 7d85-1 6b3s-4 5sx4-2 5nuz-2 Search similar-shape structures by Omokage search (details)

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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: Fab heavy chain

L: Fab light chain

A: Single chain Fv - heavy chain

B: Single chain Fv - light chain

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	41.900, 93.280, 177.040
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Antibody , 4 types, 4 molecules HLAB

#1: Antibody	Fab heavy chain / Fragment antigen-binding Mass: 23677.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody	Fab light chain / Fragment antigen-binding Mass: 23921.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody	Single chain Fv - heavy chain Mass: 13365.833 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Antibody	Single chain Fv - light chain Mass: 11773.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 2 types, 507 molecules

#5: 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
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.41 Å³/Da / Density % sol: 48.89 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 8000, 0.1M HEPES pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 1, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 1.85→64.25 Å / Num. obs: 55039 / % possible obs: 92 % / Redundancy: 4 % / R_merge(I) obs: 0.057 / Net I/σ(I): 15.25
Reflection shell	Resolution: 1.85→1.92 Å / R_merge(I) obs: 0.055 / Mean I/σ(I) obs: 2.46 / Num. unique obs: 4169

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHASER		phasing
PHENIX		refinement
PDB_EXTRACT	3.25	data extraction
xia2		data reduction
pointless		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.85→64.21 Å / FOM work R set: 0.8877 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2029	2708	4.92 %
R_work	0.1559	52294	-
obs	0.1581	55002	91.08 %

Solvent computation

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

Displacement parameters

B_iso max: 92.73 Å² / B_iso mean: 26.95 Å² / B_iso min: 8.98 Å²

Refinement step

Cycle: final / Resolution: 1.85→64.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5050	0	6	506	5562
B_iso mean	-	-	39.61	34.52	-
Num. residues	-	-	-	-	654

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5284
X-RAY DIFFRACTION	f_angle_d	1.126	7221
X-RAY DIFFRACTION	f_chiral_restr	0.081	811
X-RAY DIFFRACTION	f_plane_restr	0.005	916
X-RAY DIFFRACTION	f_dihedral_angle_d	12.113	1885

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.85-1.8837	0.2619	165	0.2182	2770	94
1.8837-1.9199	0.2594	154	0.195	2809	94
1.9199-1.9591	0.2278	154	0.1937	2750	93
1.9591-2.0017	0.2509	139	0.1859	2799	93
2.0017-2.0482	0.2326	132	0.1774	2769	93
2.0482-2.0995	0.2386	156	0.1737	2742	92
2.0995-2.1562	0.2232	135	0.1626	2754	93
2.1562-2.2197	0.2075	156	0.1546	2785	93
2.2197-2.2913	0.1922	143	0.1592	2735	92
2.2913-2.3732	0.2402	140	0.1657	2749	92
2.3732-2.4683	0.2243	163	0.1648	2763	92
2.4683-2.5806	0.2152	144	0.1631	2713	91
2.5806-2.7167	0.2106	117	0.1545	2757	91
2.7167-2.8869	0.2044	144	0.1556	2734	91
2.8869-3.1098	0.2384	158	0.158	2735	90
3.1098-3.4227	0.1753	124	0.147	2715	89
3.4227-3.9179	0.1391	132	0.1388	2733	89
3.9179-4.9359	0.1736	132	0.1251	2705	87
4.9359-64.21	0.2116	120	0.1656	2777	84

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	0.1333	-0.0569	-0.0311	0.0259	-0.0129	0.1367	-0.0533	-0.0244	-0.0389	-0.2339	-0.1713	0.085	-0.1887	-0.0974	-0.2401	0.3721	0.0906	-0.1961	0.1258	-0.0177	0.3522	38.774	23.6416	28.0243
2	0.0665	-0.0267	0.0119	0.0296	-0.0201	0.024	-0.0143	-0.068	0.0639	-0.08	-0.0611	0.0164	-0.0829	-0.1043	-0.037	0.166	0.2419	-0.0973	0.3662	-0.1855	0.3449	33.5309	19.1704	38.9097
3	0.0394	0.097	0.0224	0.3329	0.0646	0.0294	-0.1049	-0.0372	0.0595	-0.1993	-0.019	0.029	-0.1621	-0.0966	-0.0337	0.1624	0.0476	-0.0322	0.154	-0.0364	0.1504	46.7418	18.5858	38.6983
4	0.0242	0.1033	0.0618	0.4564	0.2292	0.1356	-0.1275	-0.0482	0.0934	-0.4154	-0.0373	0.025	-0.3506	-0.2062	-0.1547	0.3298	0.1829	-0.1664	0.1109	-0.09	0.317	42.3728	26.2599	35.8857
5	0.017	-0.0129	-0.0089	0.1414	0.0551	0.0446	-0.1231	-0.1202	0.0328	-0.1666	-0.2041	0.1596	-0.0953	-0.2169	-0.0477	0.1866	0.0338	-0.035	0.2187	-0.045	0.1846	40.9055	12.1476	36.3793
6	0.1147	-0.0318	-0.0995	0.0094	0.0252	0.0895	-0.0464	0.1173	-0.1031	0.0767	-0.0922	0.0201	-0.158	-0.0119	-0.0253	0.4605	0.018	-0.1279	0.193	-0.0022	0.31	39.5632	16.8247	5.953
7	0.015	-0.0024	-0.0041	0.0067	0.0029	0.01	0.0261	0.0554	-0.1037	0.0309	0.0107	0.0633	-0.1643	-0.0634	-0.0005	0.391	0.0397	-0.1312	0.1943	0.0018	0.2244	38.2283	8.4676	3.5664
8	0.001	-0.0045	-0.0009	0.0096	0.0034	0.0089	-0.0609	0.0346	-0.0356	0.1015	-0.1151	-0.0027	-0.2992	-0.1251	0.0001	0.4104	-0.005	-0.0303	0.2347	-0.0231	0.3246	35.1601	12.9215	12.5211
9	0.0464	-0.0383	-0.0195	0.0291	0.0248	0.0641	-0.0392	-0.0355	-0.0107	0.0093	0.0019	-0.0561	-0.2909	-0.0291	-0	0.3126	-0.0075	-0.057	0.2022	-0.025	0.2233	40.8914	8.7167	8.7916
10	0.0013	0.0019	-0.0016	0.0239	-0.0412	0.0676	0.0224	0.2034	-0.0499	0.1353	0.1042	0.1316	-0.2517	-0.2535	0.0132	0.3242	0.0465	-0.0786	0.3206	-0.0899	0.3298	29.3045	6.9336	4.8991
11	0.0061	0.0031	0.0051	0.0023	0.0038	0.0043	0.0826	0.1671	-0.0098	0.086	0.0161	0.022	-0.0768	0.0144	0	0.377	0.0824	-0.114	0.3186	-0.0601	0.3744	29.6436	12.4122	1.838
12	0.1733	-0.0963	-0.0857	0.1842	0.0574	0.1203	0.0019	-0.0201	0.0199	-0.0285	-0.0123	0.0124	0.0053	-0.0023	-0	0.1151	0.0006	-0.0174	0.1129	-0.024	0.1271	51.5737	-0.0426	35.0034
13	0.1153	0.0396	0.0957	0.176	0.0942	0.1	-0.0244	0.132	0.1319	-0.1256	-0.0008	-0.0756	-0.2548	0.0394	-0.0008	0.2712	0.0118	-0.0286	0.1967	0.0498	0.1384	48.9606	5.0036	-1.2318
14	0.0096	-0.0152	-0.015	0.0257	0.0261	0.0227	-0.0048	0.0448	0.0156	0.0477	-0.0685	0.1173	0.0273	-0.1336	0.0001	0.2241	0.0189	0.0392	0.2967	-0.017	0.1835	45.1398	19.0583	78.1385
15	-0.001	0.0079	0.0102	0.0232	0.0037	0.0348	0.0552	-0.0111	-0.1762	0.0956	-0.0889	0.1026	0.1001	-0.2535	-0.0006	0.1078	-0.0332	0.0089	0.2895	-0.0159	0.1781	40.3916	13.6534	66.5065
16	0.025	-0.024	-0.0074	0.0191	0.003	0.0125	-0.0008	0.0154	0.0758	-0.0219	0.0332	-0.1015	-0.1106	-0.0263	0	0.1577	-0.0209	0.012	0.1776	0.0002	0.177	52.9758	17.8885	69.0891
17	0.0008	0.0037	-0.0078	0.0079	-0.0169	0.0309	-0.0514	-0.101	-0.1131	-0.0134	0.0381	0.0043	0.0801	-0.0006	0	0.1466	-0.0401	0.0044	0.1198	0.0021	0.1361	51.0834	9.9136	65.3272
18	0.0078	-0.0092	0.0016	0.0083	-0.001	0.0093	-0.0955	0.0396	-0.1031	0.0067	-0.0394	0.0121	0.0788	-0.0285	0.0001	0.19	0.0101	0.0057	0.1947	0.0073	0.1858	58.6077	8.5348	70.6656
19	0.0007	-0.003	0.001	0.0085	-0.0117	0.0137	0.006	-0.0241	-0.0406	0.1265	-0.0802	0.0497	0.0798	-0.1984	0	0.16	-0.0607	0.0371	0.2484	0.0078	0.175	43.668	8.9857	72.4105
20	0.0655	0.013	-0.0616	0.0662	-0.0057	0.0468	-0.0151	-0.0214	-0.0761	0.0496	-0.0499	-0.0185	0.0261	0.0239	-0	0.1171	0.002	-0.002	0.1498	-0.0192	0.1179	50.7585	18.4808	66.4437
21	0.008	-0.004	0.0052	0.0057	-0.0051	0.0195	0.0156	0.0339	-0.0089	0.0251	-0.0319	0.0421	-0.0155	-0.0041	0.0001	0.2549	0.0204	0.0123	0.208	-0.0105	0.0985	51.6419	21.5816	83.3401
22	0.0003	-0.0007	-0.0037	0.0082	-0.0134	0.0289	0.0075	-0.0712	-0.0344	0.0408	0.0087	-0.0434	-0.0907	0.0362	-0	0.127	-0.01	-0.0084	0.1659	-0.0012	0.1764	66.5669	27.8636	62.9097
23	0.0271	0.0107	0.018	0.0029	0.0067	0.0062	0.0603	-0.1389	-0.0038	-0.007	-0.0127	-0.0198	0.0522	0.0952	-0	0.1241	0.0208	0.0081	0.1125	-0.0028	0.17	63.0625	37.5864	56.6911
24	0.0159	0.0103	-0.0049	0.046	-0.0323	0.0171	0.0049	0.0579	-0.0567	0.0571	-0.0188	0.0577	-0.0665	0.0324	0.0236	0.0855	0.0202	0.0096	0.1262	-0.014	0.1643	59.958	23.367	56.0323
25	0.0006	-0.0023	-0.0035	0.0088	-0.002	0.0144	0.0284	-0.1737	0.1101	0.0235	-0.0174	0.0871	-0.0107	-0.1045	0.0096	0.1254	0.0016	0.0275	0.2249	-0.0576	0.1217	49.8042	31.0029	64.4894
26	0.0046	0.0005	0.001	0.011	0.005	-0.0005	-0.1126	0.0642	0.0131	-0.0835	-0.0164	0.1813	-0.0536	0.0419	0	0.12	0.0067	-0.0103	0.1593	-0.0122	0.1836	52.2307	31.3569	51.0503
27	0.0294	0.0316	0.0036	0.0303	-0.0011	0.0122	-0.0179	0.0602	-0.0301	0.0442	-0.0197	0.0757	-0.0674	-0.0382	0	0.1235	0.0269	0.0124	0.1241	-0.003	0.1361	57.6982	37.0632	56.2277
28	0.0055	0.0006	0.0027	0.0055	0.0032	0.0011	0.0847	0.0274	-0.0052	0.0312	-0.0319	-0.0384	-0.0367	0.0849	0	0.1138	-0.013	0.0069	0.118	-0.0064	0.1453	58.1397	28.4064	62.3453
29	0.0222	0.0231	-0.0513	0.0248	-0.0654	0.2269	0.0316	-0.0506	-0.0679	-0.0073	-0.0501	0.0429	-0.0338	0.1487	-0.0078	0.0791	0.0149	-0.0013	0.1103	-0.0206	0.1489	60.2445	22.8869	61.6133

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 17 )	H	1 - 17
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 18 through 32 )	H	18 - 32
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 33 through 63 )	H	33 - 63
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 64 through 87 )	H	64 - 87
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 88 through 109 )	H	88 - 109
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 110 through 134 )	H	110 - 134
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 135 through 145 )	H	135 - 145
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 146 through 157 )	H	146 - 157
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 158 through 184 )	H	158 - 184
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 185 through 202 )	H	185 - 202
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 203 through 213 )	H	203 - 213
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 1 through 113 )	L	1 - 113
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 114 through 211 )	L	114 - 211
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 1 through 17 )	A	1 - 17
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 18 through 32 )	A	18 - 32
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 33 through 44 )	A	33 - 44
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 45 through 56 )	A	45 - 56
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 57 through 66 )	A	57 - 66
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 67 through 82 )	A	67 - 82
20	X-RAY DIFFRACTION	20	chain 'A' and (resid 82A through 106 )	A	82
21	X-RAY DIFFRACTION	21	chain 'A' and (resid 107 through 112 )	A	107 - 112
22	X-RAY DIFFRACTION	22	chain 'B' and (resid -2 through 12 )	B	-2 - 12
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 13 through 25 )	B	13 - 25
24	X-RAY DIFFRACTION	24	chain 'B' and (resid 26 through 38 )	B	26 - 38
25	X-RAY DIFFRACTION	25	chain 'B' and (resid 39 through 48 )	B	39 - 48
26	X-RAY DIFFRACTION	26	chain 'B' and (resid 49 through 67 )	B	49 - 67
27	X-RAY DIFFRACTION	27	chain 'B' and (resid 68 through 83 )	B	68 - 83
28	X-RAY DIFFRACTION	28	chain 'B' and (resid 84 through 90 )	B	84 - 90
29	X-RAY DIFFRACTION	29	chain 'B' and (resid 91 through 105 )	B	91 - 105

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Antibody , 4 types, 4 molecules HLAB

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Non-polymers , 2 types, 507 molecules

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-Antibody , 4 types, 4 molecules HLAB

-Non-polymers , 2 types, 507 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

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-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

-
Structure viewers

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Viewer log

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This page

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This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

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Downloads & links

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Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Antibody , 4 types, 4 molecules HLAB

-
Non-polymers , 2 types, 507 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi