PDB-4plj: Hepatitis E Virus E2s domain (Genotype IV) in complex with a neut...

ID or keywords:

Entry

Database: PDB / ID: 4plj

Title

Hepatitis E Virus E2s domain (Genotype IV) in complex with a neutralizing antibody 8G12

Components

8G12 heavy chain
8G12 light chain
Capsid proteinCapsid

Keywords

VIRAL PROTEIN/IMMUME SYSTEM /

Complex /

neutralizing antibody /

VIRAL PROTEIN-IMMUME SYSTEM complex

Function / homology

Function and homology information

structural molecule activity /

RNA binding / identical protein binding
Similarity search - Function

Biological species

Hepatitis E virus

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.3 Å

Authors

Tang, X.H. / Li, S.W. / Sivaraman, J.

Citation

Journal: Cell Res. / Year: 2015
Title: Structural basis for the neutralization of hepatitis E virus by a cross-genotype antibody
Authors: Gu, Y. / Tang, X. / Zhang, X. / Song, C. / Zheng, M. / Wang, K. / Zhang, J. / Ng, M.H. / Hew, C.L. / Li, S. / Xia, N. / Sivaraman, J.

History

Deposition	May 18, 2014	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Apr 15, 2015	Provider: repository / Type: Initial release
Revision 1.1	May 13, 2015	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4plj.cif.gz	455.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4plj.ent.gz	389.7 KB	Display	PDB format
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Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pl/4plj ftp://data.pdbj.org/pub/pdb/validation_reports/pl/4plj	HTTPS FTP

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Related structure data

Related structure data	4plkC C: citing same article (ref.)
Similar structure data	4plk-2 4plk-1 7m7w-1 7m7w-2 2nvw-2 4res-2 3slc-d 6fla-d 4res-1 4ygc-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#170 - Feb 2014 Broadly Neutralizing Antibodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Capsid protein

B: Capsid protein

L: 8G12 light chain

H: 8G12 heavy chain

C: 8G12 light chain

D: 8G12 heavy chain

128 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	56.775, 89.459, 137.636
Angle α, β, γ (deg.)	90.00, 95.90, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Capsid protein / Capsid Mass: 15988.812 Da / Num. of mol.: 2 / Fragment: E2S domain, UNP residues 93-240 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis E virus / Production host: Escherichia coli (E. coli) / References: UniProt: D3VV84
#2: Antibody	8G12 light chain Mass: 23415.779 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody	8G12 heavy chain Mass: 24788.795 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.71 Å³/Da / Density % sol: 54.6 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion / Details: 14% PEG 1500

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.3→30 Å / Num. obs: 61168 / % possible obs: 99.8 % / Redundancy: 5.7 % / Net I/σ(I): 14.3

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data processing

Refinement

Resolution: 2.3→29.137 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 26.36 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2422	1991	3.27 %
R_work	0.187	-	-
obs	0.1888	60870	99.81 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.3→29.137 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8768	0	0	364	9132

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	8992
X-RAY DIFFRACTION	f_angle_d	1.158	12262
X-RAY DIFFRACTION	f_dihedral_angle_d	14.363	3162
X-RAY DIFFRACTION	f_chiral_restr	0.045	1385
X-RAY DIFFRACTION	f_plane_restr	0.006	1555

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 (%)
2.3-2.3575	0.3461	141	0.2771	4190	X-RAY DIFFRACTION	100
2.3575-2.4212	0.3407	142	0.2608	4160	X-RAY DIFFRACTION	100
2.4212-2.4924	0.3468	141	0.2505	4206	X-RAY DIFFRACTION	100
2.4924-2.5728	0.2933	142	0.2371	4190	X-RAY DIFFRACTION	100
2.5728-2.6647	0.2473	141	0.2238	4160	X-RAY DIFFRACTION	100
2.6647-2.7713	0.2781	141	0.2096	4201	X-RAY DIFFRACTION	100
2.7713-2.8973	0.2773	142	0.2019	4163	X-RAY DIFFRACTION	100
2.8973-3.0499	0.2532	142	0.1912	4214	X-RAY DIFFRACTION	100
3.0499-3.2408	0.2395	142	0.1805	4195	X-RAY DIFFRACTION	100
3.2408-3.4906	0.2115	142	0.1732	4197	X-RAY DIFFRACTION	100
3.4906-3.8412	0.2231	143	0.1746	4230	X-RAY DIFFRACTION	100
3.8412-4.3954	0.2177	144	0.154	4236	X-RAY DIFFRACTION	100
4.3954-5.5316	0.1854	142	0.1521	4218	X-RAY DIFFRACTION	100
5.5316-29.1389	0.2511	146	0.1837	4319	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	1.5032	-0.3147	-0.375	2.7753	0.2256	2.0129	0.012	0.2012	0.2705	0.0084	0.019	0.1956	-0.0497	-0.1052	-0.0531	0.2341	-0.0247	-0.0235	0.4667	0.1359	0.3317	-9.8689	-10.5728	23.9408
2	2.8173	1.2347	1.716	2.2897	0.6423	5.7239	-0.019	0.2643	0.8402	-0.1056	0.0268	0.3811	-0.5042	-0.8218	0.0175	0.3152	0.0118	-0.0084	0.4864	0.2117	0.6669	-11.4178	0.4078	20.8758
3	2.2243	0.1669	0.1473	1.4397	-0.7123	1.3226	-0.0972	0.599	0.1244	-0.1899	0.1453	0.2214	0.0395	-0.3069	-0.0499	0.2129	-0.0527	-0.0281	0.4696	0.0705	0.2748	-8.4642	-16.2366	21.1269
4	2.989	1.8596	-1.2014	6.5645	-0.2889	0.4775	0.1096	1.1662	-0.1244	0.0447	-0.2255	-0.0563	-0.6046	-0.027	0.0597	0.2303	0.0375	-0.0252	0.6141	0.1128	0.3439	-3.2397	-6.8221	18.2655
5	8.8721	3.881	-1.0812	9.9723	-1.1933	8.0353	0.0538	-1.0421	1.1754	0.052	0.1627	0.6552	-0.9814	0.3353	-0.1352	0.3766	-0.0713	0.0114	0.2653	-0.0931	0.3873	9.9823	-2.5264	37.5685
6	1.4476	-0.162	-0.6027	1.7008	0.7111	1.9903	0.0419	0.2098	0.2495	-0.185	0.0318	-0.3106	0.0481	0.3721	-0.0675	0.2679	-0.0119	-0.0001	0.5748	0.1059	0.3094	17.7549	-14.25	21.8053
7	7.3294	-0.5496	0.2275	2.1764	0.6663	0.8112	0.0461	0.338	0.9139	-0.0089	0.0539	-0.5855	-0.7488	0.5724	-0.1378	0.4947	-0.1965	0.0186	0.4031	0.0223	0.5635	17.3884	-1.1182	29.9095
8	2.4648	-2.5525	-1.9309	5.7198	2.5462	3.9215	-0.3527	-0.6153	0.0222	0.5614	0.3518	-0.4056	0.1467	0.5661	-0.0314	0.2613	0.0196	-0.0699	0.6282	0.0373	0.2951	19.6326	-13.7048	37.8504
9	1.5515	-0.759	-0.3767	1.3151	-0.6158	1.5745	-0.1055	-0.106	0.0938	-0.0553	-0.0846	-0.1942	0.0122	0.555	0.169	0.2036	-0.0392	-0.0108	0.488	0.0855	0.2639	13.4106	-16.7739	23.111
10	3.4886	0.8982	-4.387	1.6166	0.7874	7.959	-0.1511	-0.0958	0.1389	0.1255	0.0889	-0.1914	0.3571	-0.3657	-0.0634	0.2124	-0.067	-0.0493	0.371	0.0634	0.2894	8.9198	-11.7651	31.5365
11	1.8589	1.5417	-1.399	3.9966	-0.8654	1.6856	-0.1832	-0.6474	-0.5082	0.1977	-0.2022	-0.7674	0.3543	0.5898	0.361	0.3083	0.1107	0.0278	0.5912	0.1949	0.4746	-0.5612	-40.0612	48.4651
12	4.3415	1.7602	-2.3501	4.5578	-3.1691	5.0641	0.1877	-0.087	-0.1383	-0.701	-0.4405	0.2045	0.5748	0.8634	0.1691	0.2933	0.022	-0.0081	0.2753	0.0247	0.2862	-6.4427	-30.8885	40.4392
13	4.0218	2.0015	-1.4857	3.7176	-2.2659	2.6106	-0.0877	0.1731	-0.1818	-0.2993	-0.1116	-0.0965	0.802	0.0724	0.0905	0.5682	0.0676	0.0174	0.2866	0.1092	0.4099	-24.8535	-58.3009	64.8202
14	5.5028	-0.2669	0.7041	2.3821	-0.3167	2.3477	0.2136	0.119	-0.466	0.0977	-0.1664	0.1091	0.6563	-0.088	-0.0187	0.6907	-0.007	0.0275	0.337	0.0811	0.4196	-28.6443	-60.1106	65.4075
15	6.0388	4.0472	-2.0447	6.0455	-0.1991	1.1895	0.4117	-0.9161	0.6023	0.233	-0.4545	0.4776	-0.3684	-0.3742	-0.0898	0.305	0.0497	0.0417	0.3643	-0.0063	0.3078	-24.6635	-24.8352	54.5284
16	4.64	0.0049	-0.6781	3.3973	-0.7719	4.2095	0.1205	-0.3085	0.3746	0.0325	0.0196	0.1064	-0.2627	0.0678	-0.1165	0.2178	0.0093	0.0264	0.3033	0.032	0.2968	-15.8053	-21.4304	46.8804
17	4.862	2.6643	-1.1914	2.7577	-0.9297	2.3462	0.0864	-0.0228	0.0418	0.036	-0.1061	-0.0388	-0.0038	0.4256	0.0156	0.2902	0.0212	0.0036	0.3158	0.0558	0.2888	-14.1143	-27.0415	49.3961
18	3.1647	0.8251	-1.7664	1.0605	0.2053	2.9326	0.3183	-0.343	-0.4732	-0.134	0.499	0.9049	1.189	-0.1143	-0.7547	0.6227	0.025	-0.032	0.2162	-0.0226	0.3409	-32.6298	-46.9043	69.8671
19	2.7062	-1.3577	-0.416	2.5204	-2.0978	3.5189	0.002	0.1906	0.1774	0.2796	-0.2022	-0.2534	0.0928	0.2596	0.2271	0.4031	-0.0126	-0.0354	0.244	0.0982	0.386	-26.0278	-45.2699	68.2459
20	4.9215	-3.0078	4.0306	7.4924	-5.0198	2.9949	-0.3183	-0.5591	0.2503	0.2423	-0.0655	-0.312	0.0223	-0.2963	0.4701	0.5645	0.0883	0.0343	0.3832	-0.0119	0.2603	-28.2647	-43.6362	78.6843
21	0.9992	0.0335	-0.4591	1.2028	-1.1361	2.2178	-0.1098	0.6383	-0.1859	-0.5938	0.1553	0.0528	0.47	-0.3938	-0.0898	0.5543	-0.1763	-0.0341	0.9469	-0.028	0.3451	8.0972	-20.9168	-9.567
22	0.8289	0.3463	0.0223	2.3359	0.5269	1.8478	0.2105	1.3551	0.5044	-0.3054	-0.0966	0.2319	-0.2251	-1.424	-0.0803	0.5211	0.0112	-0.0463	1.0926	0.1236	0.3632	6.0002	-8.9196	-14.2894
23	1.7315	0.8196	-1.7505	1.6396	0.9616	3.2858	-0.2628	0.6982	-0.1699	-0.6286	-0.051	0.0781	0.1033	-0.8299	0.2955	0.6177	-0.1559	0.0195	0.9974	0.0066	0.3822	9.1194	-18.1812	-14.9134
24	8.606	0.31	0.0904	2.2195	-0.4223	3.4358	0.0322	-1.2607	-0.6099	-0.4475	-0.2324	-0.4709	1.0834	0.6546	0.1891	0.9128	0.2283	0.1933	0.8402	0.0773	0.4888	34.5766	-17.506	-37.1755
25	4.968	1.8239	2.0801	5.8858	-0.6413	4.2943	0.1753	-0.1071	-1.0496	-0.8038	0.6856	-0.976	0.6141	-0.4804	-0.9456	1.039	0.0046	0.1775	0.629	0.1313	0.9854	37.5147	-25.6168	-36.272
26	5.2132	0.2422	0.3633	2.1992	0.4019	2.6681	0.3262	-0.0722	-0.5428	-0.0682	-0.2679	-0.3979	0.4781	-0.1409	-0.1528	0.9619	0.1091	0.1533	0.7015	0.0681	0.4815	34.0737	-18.3091	-34.5094
27	6.8336	0.8628	1.4392	3.1951	-0.7118	3.4071	-0.1265	0.9333	-0.0515	-0.8662	0.37	-0.9077	0.3991	0.9437	-0.1201	1.3048	0.1353	0.4445	0.9336	-0.0621	0.9095	37.1643	-24.1878	-45.379
28	4.9844	-1.7929	-1.514	2.4838	0.8755	2.5509	0.1496	-0.0585	0.407	-0.1654	0.0449	-0.2734	-0.479	1.21	-0.1857	0.3583	-0.0883	-0.0031	1.0006	0.2118	0.5552	31.5732	-2.3355	-6.4137
29	3.3582	-1.0455	-1.0583	2.0167	-0.8101	2.8252	0.4669	0.3941	0.5909	-0.7324	-0.3781	-0.5187	-0.378	0.192	-0.0803	0.4139	-0.0522	0.0702	0.6855	0.1946	0.421	19.0659	-3.7054	-3.7186
30	3.0477	0.0054	-0.2323	3.3507	1.1378	3.3222	0.0882	-0.2146	-0.0418	0.1881	-0.0404	-0.0552	-0.0899	0.5226	-0.0348	0.3099	-0.0965	0.0029	0.6863	0.087	0.3483	20.5703	-7.419	5.1952
31	3.0829	-0.5458	0.3734	6.7604	-0.4224	2.6926	-0.105	0.2913	0.6203	-0.054	0.1663	-0.0685	-0.5116	0.7679	-0.0789	0.3982	-0.2209	-0.0065	0.9658	0.1956	0.5159	27.411	-0.9197	2.8837
32	2.2318	-5.7403	-0.2655	4.5056	-1.3963	2.585	0.0296	0.781	-0.1457	-0.0096	-0.333	0.0398	0.2038	0.5613	0.3208	0.4159	-0.0395	0.0069	1.0006	0.1634	0.4259	27.7086	-9.8275	-4.1915
33	4.6647	-0.374	-2.4541	1.0223	-0.0777	1.7525	0.0974	0.9367	0.7653	-0.2497	-0.1369	-0.0732	-0.1609	0.1897	-0.0552	0.3616	-0.0154	-0.0044	0.7334	0.1914	0.3907	15.2085	-4.7409	-4.1208
34	1.1763	0.4966	-0.7533	2.554	-0.7198	0.5611	-0.0152	0.6051	-0.0682	-0.5041	-0.3721	-0.4442	0.1	1.2558	0.3899	0.5273	0.1775	0.1971	0.8027	0.044	0.4618	40.0671	-8.6562	-30.7438
35	3.6484	0.692	-0.2849	2.9653	0.8072	5.1445	-0.2711	-0.9668	0.1926	-0.2696	-0.1777	-0.0391	0.0307	0.5355	0.423	0.5317	0.0785	0.045	0.6801	-0.0092	0.346	31.811	-6.0028	-31.3225
36	2.7325	0.6819	-0.8808	1.7409	0.7273	0.8195	-0.0115	-0.2016	-0.5429	0.0453	0.0992	-0.0793	0.7692	1.0206	-0.1056	0.7338	0.1869	0.0944	1.1596	0.1338	0.5087	34.8211	-12.8135	-28.3822
37	5.7	-0.7656	-1.3405	6.0416	-1.1093	2.8792	0.3696	-0.7184	0.7671	-0.5862	0.1669	-0.3776	0.6963	-0.3504	-0.5873	0.5801	0.0419	0.0982	0.6168	-0.0245	0.47	33.5255	-0.5225	-37.0861
38	4.8198	0.8929	3.297	3.7982	1.6466	2.0365	0.4974	0.8608	0.24	-0.6471	0.3702	-0.9231	-0.087	0.9309	-0.5759	0.7963	0.0205	0.1816	0.6105	0.1329	0.5759	39.5994	-0.5742	-36.6601

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 459 through 502 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 503 through 527 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 528 through 594 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 595 through 606 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 459 through 469 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 470 through 502 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 503 through 515 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 516 through 533 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 534 through 594 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 595 through 605 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 1 through 90 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 91 through 101 )
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 102 through 155 )
14	X-RAY DIFFRACTION	14	chain 'L' and (resid 156 through 212 )
15	X-RAY DIFFRACTION	15	chain 'H' and (resid 1 through 22 )
16	X-RAY DIFFRACTION	16	chain 'H' and (resid 23 through 81 )
17	X-RAY DIFFRACTION	17	chain 'H' and (resid 82 through 119 )
18	X-RAY DIFFRACTION	18	chain 'H' and (resid 120 through 144 )
19	X-RAY DIFFRACTION	19	chain 'H' and (resid 145 through 194 )
20	X-RAY DIFFRACTION	20	chain 'H' and (resid 195 through 223 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 1 through 38 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 39 through 61 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 62 through 113 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 114 through 146 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 147 through 163 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 164 through 188 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 189 through 211 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 1 through 21 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 22 through 42 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 43 through 62 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 63 through 81 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 82 through 97 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 98 through 119 )
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 120 through 144 )
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 145 through 175 )
36	X-RAY DIFFRACTION	36	chain 'D' and (resid 176 through 194 )
37	X-RAY DIFFRACTION	37	chain 'D' and (resid 195 through 212 )
38	X-RAY DIFFRACTION	38	chain 'D' and (resid 213 through 223 )

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