PDB-6j5f: Complex structure of MAb 4.2-scFv with tick-borne encephalitis vi...

ID or keywords:

Entry

Database: PDB / ID: 6j5f

Title

Complex structure of MAb 4.2-scFv with tick-borne encephalitis virus envelope protein Domain III

Components

Envelope protein
antibody heavy chain
antibody light chain

Keywords

VIRAL PROTEIN/IMMUNE SYSTEM / protective and neutralizing antibody / flavivirus envelope protein / ANTIVIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex

Function / homology

Function and homology information

host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane / membrane
Similarity search - Function

Biological species

Tick-borne encephalitis virus

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.801 Å

Authors

Yang, X. / Qi, J. / Peng, R. / Dai, L. / Gould, E.A. / Tien, P. / Gao, G.F.

Citation

Journal: J. Virol. / Year: 2019
Title: Molecular Basis of a Protective/Neutralizing Monoclonal Antibody Targeting Envelope Proteins of both Tick-Borne Encephalitis Virus and Louping Ill Virus.
Authors: Yang, X. / Qi, J. / Peng, R. / Dai, L. / Gould, E.A. / Gao, G.F. / Tien, P.

History

Deposition	Jan 10, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 6, 2019	Provider: repository / Type: Initial release
Revision 1.1	Mar 13, 2019	Group: Data collection / Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Apr 17, 2019	Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3	Nov 22, 2023	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 1.4	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6j5f.cif.gz	147.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6j5f.ent.gz	115.6 KB	Display	PDB format
PDBx/mmJSON format	6j5f.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6j5f_validation.pdf.gz	440.6 KB	Display	wwPDB validaton report
Full document	6j5f_full_validation.pdf.gz	443.1 KB	Display
Data in XML	6j5f_validation.xml.gz	17.5 KB	Display
Data in CIF	6j5f_validation.cif.gz	25.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j5/6j5f ftp://data.pdbj.org/pub/pdb/validation_reports/j5/6j5f	HTTPS FTP

-
Related structure data

Related structure data	6j5cC 6j5dC 6j5gC 1svbS 5grjS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4dwh-2 7ly0-d 6tru-4 6ymq-4 1g7l-d 3kvx-d 3doe-d 3dvx-d 1jhl-d 6j5d-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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) #103 - Jul 2008 Dengue Virus similarity (9) #197 - May 2016 Zika Virus similarity (9)

Deposited unit

A: Envelope protein

H: antibody heavy chain

L: antibody light chain

36.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, homology

Unit cell

Length a, b, c (Å)	92.668, 95.461, 99.970
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

Components on special symmetry positions

ID	Model	Components
1	1	A-577- HOH

#1: Protein	Envelope protein Mass: 11032.542 Da / Num. of mol.: 1 / Fragment: Domain III Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tick-borne encephalitis virus Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A096YGU7
#2: Antibody	antibody heavy chain Mass: 13169.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Antibody	antibody light chain Mass: 11977.288 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.06 Å³/Da / Density % sol: 59.74 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 1% w/v tryptone, 0.05M HEPES sodium pH 7.0, 20% w/v PEG 3350

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97853 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. obs: 41293 / % possible obs: 99.9 % / Redundancy: 12.7 % / B_iso Wilson estimate: 24.68 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.103 / Net I/σ(I): 27.6
Reflection shell	Resolution: 1.8→1.86 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 9.4 / Num. unique obs: 4076 / CC_1/2: 0.807 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1SVB, 5GRJ

1svb

5grj

Resolution: 1.801→39.954 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.97

	R_factor	Num. reflection	% reflection
R_free	0.1924	1949	5.01 %
R_work	0.1794	-	-
obs	0.18	38897	94.07 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.801→39.954 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2484	0	0	354	2838

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2551
X-RAY DIFFRACTION	f_angle_d	0.871	3468
X-RAY DIFFRACTION	f_dihedral_angle_d	16.849	916
X-RAY DIFFRACTION	f_chiral_restr	0.077	373
X-RAY DIFFRACTION	f_plane_restr	0.004	443

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 (%)
1.8006-1.8457	0.2732	133	0.2312	1930	X-RAY DIFFRACTION	70
1.8457-1.8956	0.2398	139	0.2284	2118	X-RAY DIFFRACTION	78
1.8956-1.9513	0.2423	145	0.2164	2270	X-RAY DIFFRACTION	84
1.9513-2.0143	0.2003	147	0.2029	2494	X-RAY DIFFRACTION	90
2.0143-2.0863	0.2457	150	0.1955	2706	X-RAY DIFFRACTION	97
2.0863-2.1698	0.2099	123	0.1921	2749	X-RAY DIFFRACTION	99
2.1698-2.2686	0.2196	159	0.194	2771	X-RAY DIFFRACTION	100
2.2686-2.3882	0.2066	148	0.1942	2809	X-RAY DIFFRACTION	100
2.3882-2.5378	0.2031	164	0.1975	2751	X-RAY DIFFRACTION	100
2.5378-2.7337	0.2125	118	0.1915	2832	X-RAY DIFFRACTION	100
2.7337-3.0087	0.1923	111	0.1871	2843	X-RAY DIFFRACTION	100
3.0087-3.4438	0.1991	139	0.1696	2848	X-RAY DIFFRACTION	100
3.4438-4.338	0.1661	104	0.1536	2887	X-RAY DIFFRACTION	100
4.338-39.9643	0.1386	169	0.1548	2940	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	0.6928	0.242	-0.1457	1.0672	0.4259	0.743	-0.0358	0.0558	0.0177	0.0014	0.0467	-0.2227	-0.1087	0.2338	0.0594	0.0707	-0.0485	-0.0091	0.1869	-0.0037	0.1213	33.9477	12.4006	45.6552
2	0.3961	-0.1281	-0.4038	0.5441	-0.1702	0.5881	0.0378	-0.0888	0.0178	0.3651	0.1637	-0.2905	-0.3241	0.5704	0.0892	0.1864	-0.1009	-0.0437	0.1982	0.0026	0.1799	30.6128	22.3174	41.5873
3	0.3843	-0.4591	-0.0237	0.5767	-0.0131	0.0489	-0.0501	-0.0935	-0.177	0.1419	0.003	0.5297	0.0219	-0.2924	-0.0035	0.1716	-0.0269	-0.0136	0.1394	-0.0113	0.2082	25.396	11.2378	58.488
4	0.7001	-0.0053	0.477	1.7688	0.0394	0.2986	-0.0254	0.1505	0.0783	0.3897	-0.0043	-0.356	-0.273	0.3372	0.0748	0.1545	-0.0823	-0.0567	0.2529	0.0068	0.1688	34.7911	14.0915	50.8981
5	0.1951	0.0558	-0.2013	0.1864	0.1371	0.3808	-0.059	-0.0657	0.0766	0.2252	-0.0502	-0.3429	0.1316	0.0019	-0.0067	0.1691	0.0015	-0.0696	0.1611	-0.0018	0.1403	30.8151	3.7789	54.0064
6	0.0296	0.0196	-0.0088	0.0989	0.0682	0.0609	-0.0502	0.2684	-0.0247	-0.1632	-0.0029	0.5012	-0.0899	-0.4371	-0.002	0.1767	0.0077	0.0443	0.1826	0.0392	0.2341	11.314	31.4398	23.4063
7	0.0379	0.0436	-0.0067	0.0473	0.0116	0.04	-0.0313	0.2004	0.042	-0.2527	0.0283	-0.152	-0.2133	0.2062	0	0.2688	-0.0373	0.0551	0.2107	0.0202	0.1545	23.3787	25.0171	5.1132
8	0.3236	-0.227	-0.0517	0.1596	-0.0928	0.4113	-0.0419	0.0951	0.1967	0.0293	0.1453	0.0657	-0.2617	-0.1436	0.0057	0.2764	-0.0268	0.0445	0.1392	-0.0019	0.1951	19.0617	31.8954	22.1359
9	0.2384	-0.1788	0.1452	0.1787	-0.1315	0.0945	-0.047	0.0016	0.0552	-0.0011	0.0403	0.038	-0.197	-0.0251	-0.0021	0.1663	-0.0545	0.0208	0.1175	0.0108	0.1215	19.7177	24.966	26.1894
10	0.3304	0.068	-0.2419	0.3294	-0.3713	0.4864	-0.0326	0.0487	-0.0796	-0.0996	-0.017	-0.1299	0.0323	0.0701	-0.0513	0.1489	-0.0552	0.0077	0.1279	0.0166	0.12	23.5628	18.9661	23.8531
11	0.1867	0.1423	-0.025	0.1087	-0.0289	0.0614	0.1572	-0.1005	-0.3979	-0.0915	-0.3139	-0.6662	0.4997	0.4753	0.0019	0.216	0.0092	0.0272	0.1985	0.033	0.2507	30.4412	14.1033	18.8998
12	0.6254	-0.0495	0.3499	0.1376	-0.1236	0.2594	0.0591	0.0475	0.1652	-0.0954	-0.034	-0.235	-0.3081	0.1645	-0.0393	0.2281	-0.0733	0.0356	0.1297	0.0089	0.1731	26.1156	30.6417	21.3008
13	0.4184	0.1685	-0.0113	0.6001	-0.5456	0.523	0.0029	0.0763	0.0343	-0.0238	0.0378	-0.0852	0.2147	-0.04	0.0122	0.1697	-0.0408	0.0203	0.1231	0.0015	0.1176	20.965	19.8665	16.0624
14	0.0552	0.0753	0.0136	0.1338	-0.1473	0.2321	-0.0335	-0.1271	0.2156	0.152	0.0038	0.0773	-0.3189	-0.1083	-0.0031	0.1527	-0.0333	-0.0007	0.1377	0.0068	0.1425	14.9756	22.4374	30.0484
15	0.0091	-0.0419	-0.0362	0.4263	0.3472	0.2888	-0.2259	0.3215	-0.0678	-0.1448	-0.006	0.0647	0.2533	0.0177	-0.0897	0.2545	-0.0733	0.0462	0.1904	0.0114	0.093	19.8635	21.1341	5.086
16	1.2491	-0.0282	-0.2494	0.1091	-0.3462	1.2861	0.1408	0.093	-0.3434	-0.2179	0.1211	-0.4044	-0.23	0.0274	0.2624	0.1216	-0.0398	0.05	0.1038	-0.051	0.2186	16.938	3.1855	27.1116
17	0.0322	-0.0213	-0.0255	0.142	-0.0561	0.042	0.0103	0.0018	-0.09	-0.1599	0.0414	0.2846	-0.0997	0.1086	-0	0.1244	-0.0103	-0.0274	0.1493	0.0094	0.2328	-4.2883	4.1725	22.6037
18	0.1576	0.0193	-0.1308	0.1294	-0.016	0.1003	0.079	-0.1691	-0.2787	0.1148	-0.0244	0.026	0.0128	-0.0342	-0	0.1087	-0.0249	-0.0074	0.1388	0.0166	0.1681	12.7466	4.6083	34.0071
19	0.0087	0.0343	0.0235	0.1026	0.0681	0.0557	-0.0019	0.1251	0.0957	-0.0807	0.0338	0.0908	-0.1564	-0.0029	0.0004	0.0913	-0.0339	-0.0144	0.1607	0.0244	0.1256	8.4434	13.2144	27.3929
20	0.5203	-0.1009	0.203	0.073	0.0459	0.249	-0.0758	0.1908	0.2973	-0.2385	0.099	0.1797	-0.2317	-0.1583	0.0425	0.1904	-0.0338	-0.0426	0.1737	0.0665	0.1906	5.6784	18.365	22.3519
21	0.3851	0.255	-0.2012	0.2576	-0.0289	0.2467	0.0634	-0.4245	0.1178	0.2497	-0.0968	0.2492	-0.2311	-0.1681	-0.0029	0.1225	-0.0167	0.0287	0.1768	-0.0179	0.1937	3.2727	16.4056	35.9341
22	0.2584	0.0981	-0.2623	0.1656	-0.0841	0.2507	0.06	-0.3755	-0.2801	0.1252	0.0213	0.0576	0.0648	-0.0976	0	0.1021	-0.0204	-0.0091	0.1518	0.0277	0.1848	5.5461	5.8416	34.6976
23	0.2212	0.087	0.292	0.038	0.1201	0.4006	-0.2474	-0.1077	0.5149	-0.0427	-0.0274	-0.0566	-0.546	-0.2247	-0.0209	0.2202	0.0203	-0.0234	0.2093	0.0451	0.3598	-6.2194	12.522	24.752
24	0.2768	0.3258	-0.0323	0.3513	-0.1907	0.2749	-0.081	0.0788	-0.0798	-0.0637	0.0918	-0.0092	-0.0656	0.06	0.0163	0.0868	-0.0252	-0.0016	0.1259	0.0017	0.0988	16.7869	10.9782	28.4356
25	0.0411	-0.0344	-0.1193	0.511	0.6414	0.9885	-0.0124	0.0506	-0.2741	-0.3394	0.3117	0.6311	-0.0291	-0.2394	0.1137	0.1909	-0.0692	-0.0461	0.2273	0.0678	0.3225	-1.4888	6.2261	17.7846

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 304 through 332 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 333 through 341 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 342 through 356 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 357 through 385 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 386 through 397 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 1 through 6 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 7 through 17 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 18 through 28 )
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 29 through 39 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 40 through 60 )
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 61 through 67 )
12	X-RAY DIFFRACTION	12	chain 'H' and (resid 68 through 83 )
13	X-RAY DIFFRACTION	13	chain 'H' and (resid 84 through 100 )
14	X-RAY DIFFRACTION	14	chain 'H' and (resid 101 through 113 )
15	X-RAY DIFFRACTION	15	chain 'H' and (resid 114 through 120 )
16	X-RAY DIFFRACTION	16	chain 'L' and (resid 1 through 7 )
17	X-RAY DIFFRACTION	17	chain 'L' and (resid 8 through 18 )
18	X-RAY DIFFRACTION	18	chain 'L' and (resid 19 through 32 )
19	X-RAY DIFFRACTION	19	chain 'L' and (resid 33 through 38 )
20	X-RAY DIFFRACTION	20	chain 'L' and (resid 39 through 48 )
21	X-RAY DIFFRACTION	21	chain 'L' and (resid 49 through 61 )
22	X-RAY DIFFRACTION	22	chain 'L' and (resid 62 through 75 )
23	X-RAY DIFFRACTION	23	chain 'L' and (resid 76 through 83 )
24	X-RAY DIFFRACTION	24	chain 'L' and (resid 84 through 102 )
25	X-RAY DIFFRACTION	25	chain 'L' and (resid 103 through 108 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
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

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
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