PDB-4hs6: Hepatitus C envelope glycoprotein E2 fragment 412-423 with humani...

ID or keywords:

Entry

Database: PDB / ID: 4hs6

Title

Hepatitus C envelope glycoprotein E2 fragment 412-423 with humanized and affinity-matured antibody MRCT10.v362

Components

E2-peptide
MRCT10.v362 Fab heavy chain
MRCT10.v362 Fab light chain

Keywords

IMMUNE SYSTEM

Function / homology

Function and homology information

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

Biological species

Homo sapiens (human)

Hepatitis C virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.53 Å

Authors

Eigenbrot, C. / Ultsch, M.

Citation

Journal: J.Mol.Biol. / Year: 2013
Title: Glycan shifting on hepatitis C virus (HCV) e2 glycoprotein is a mechanism for escape from broadly neutralizing antibodies.
Authors: Pantua, H. / Diao, J. / Ultsch, M. / Hazen, M. / Mathieu, M. / McCutcheon, K. / Takeda, K. / Date, S. / Cheung, T.K. / Phung, Q. / Hass, P. / Arnott, D. / Hongo, J.A. / Matthews, D.J. / ...

History

Deposition	Oct 29, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 3, 2013	Provider: repository / Type: Initial release
Revision 1.1	May 29, 2013	Group: Database references
Revision 1.2	Sep 20, 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 / struct_ncs_dom_lim / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details
Revision 1.3	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4hs6.cif.gz	372.4 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	4hs6.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/hs/4hs6 ftp://data.pdbj.org/pub/pdb/validation_reports/hs/4hs6	HTTPS FTP

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Related structure data

Related structure data	4hs8C 1fvcS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5ea0-d 5mvj-4 5mp5-4 6bzw-4 5mu2-7 3bpc-d 5ur8-d 3ggw-1 4jn1-d 4m61-2 5ik3-2 3fo9-2 4g6a-1 3fo9-1 2ck0-d 3okm-d 6bzu-3 1q9k-d 1sbs-d 3ijh-2 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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4hs8C

1fvcS

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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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) #252 - Dec 2020 Hepatitis C Virus Protease/Helicase similarity (4)

Deposited unit

Z: E2-peptide

Y: E2-peptide

A: MRCT10.v362 Fab light chain

L: MRCT10.v362 Fab light chain

B: MRCT10.v362 Fab heavy chain

H: MRCT10.v362 Fab heavy chain

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

1

Z: E2-peptide

A: MRCT10.v362 Fab light chain

B: MRCT10.v362 Fab heavy chain

defined by author&software
49.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

Y: E2-peptide

L: MRCT10.v362 Fab light chain

H: MRCT10.v362 Fab heavy chain

defined by author&software
49.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	71.091, 90.821, 72.681
Angle α, β, γ (deg.)	90.00, 109.35, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	L
1	2	B
2	2	H
1	3	Z
2	3	Y

NCS domain segments:

Component-ID: 1 / Ens-ID: 3 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 4 / Auth seq-ID: 412 - 423 / Label seq-ID: 1 - 12

Dom-ID	Auth asym-ID	Label asym-ID
1	Z	A
2	Y	B

NCS ensembles :

ID
3
1
2

#1: Protein/peptide	E2-peptide Mass: 1727.877 Da / Num. of mol.: 2 / Fragment: UNP residues 50-62 / Source method: obtained synthetically Details: This sequence occurs naturally in hepatitus C virus Source: (synth.) Hepatitis C virus / References: UniProt: Q9YK84
#2: Antibody	MRCT10.v362 Fab light chain Mass: 23846.387 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody	MRCT10.v362 Fab heavy chain Mass: 24186.021 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1059 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Nonpolymer details	E2-PEPTIDE IS BIOTINYLATED, WITH BIOTIN (BTN) ATTACHED TO THE SIDE CHAIN OF THE C-TERMINAL LYS ...E2-PEPTIDE IS BIOTINYLATED, WITH BIOTIN (BTN) ATTACHED TO THE SIDE CHAIN OF THE C-TERMINAL LYS RESIDUE. HOWEVER, SOME RESIDUES AT THE C-TERMINUS, INCLUDING BTN, ARE MISSING DUE TO DISORDER.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.22 Å³/Da / Density % sol: 44.71 %
Crystal grow	Temperature: 291 K / pH: 8.5 Details: LiCl, PEG6000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 110 K
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 23, 2011
Radiation	Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.53→50 Å / Num. obs: 131070 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / B_iso Wilson estimate: 21 Å² / R_sym value: 0.052 / Net I/σ(I): 23

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Processing

Software

Name	Version	Classification
PHASER		phasing
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1FVC

1fvc

Resolution: 1.53→50 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.957 / SU B: 3.029 / SU ML: 0.05 / Isotropic thermal model: TLS in 23 groups / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2	1318	1 %	RANDOM
R_work	0.175	-	-	-
obs	0.175	129605	99.9 %	-
all	-	130923	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 24.1 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.32 Å²	0 Å²	0.1 Å²
2-	-	0.06 Å²	-0 Å²
3-	-	-	-0.31 Å²

Refine analyze

Luzzati coordinate error free: 0.076 Å

Refinement step

Cycle: LAST / Resolution: 1.53→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6784	0	0	1059	7843

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	7063
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	4659
X-RAY DIFFRACTION	r_angle_refined_deg	1.232	1.952	9669
X-RAY DIFFRACTION	r_angle_other_deg	0.919	3.001	11456
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.843	5	920
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.269	24.384	276
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.506	15	1134
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.747	15	27
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	1109
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	7872
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1381
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.523	2.5	4472
X-RAY DIFFRACTION	r_mcbond_other	0.587	2.5	1797
X-RAY DIFFRACTION	r_mcangle_it	3.919	5	7295
X-RAY DIFFRACTION	r_scbond_it	3.76	2.5	2591
X-RAY DIFFRACTION	r_scangle_it	5.405	5	2353
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	2715	medium positional	0.73	0.5
2	B	2598	medium positional	0.81	0.5
3	Z	144	medium positional	0.49	0.5
1	A	2715	medium thermal	2.54	30
2	B	2598	medium thermal	2.58	30
3	Z	144	medium thermal	2.44	30

LS refinement shell

Resolution: 1.53→1.61 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.253	183	-
R_work	0.254	18802	-
obs	-	-	99.41 %

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	0.9948	-0.1034	-0.3836	0.5028	0.3763	0.4754	-0.0598	-0.0399	0.0835	0.0873	0.0477	-0.0535	0.0458	0.0026	0.012	0.0511	0.0289	-0.0311	0.0217	-0.0321	0.0616	34.0618	22.5296	5.076
2	1.8996	0.7373	-1.5493	0.3731	-0.6432	1.2866	0.0259	-0.1553	0.0592	0.0429	-0.0025	-0.0054	-0.0209	0.0969	-0.0234	0.0946	0.0211	0.0113	0.075	-0.0441	0.0338	14.6957	18.809	15.1505
3	0.6956	0.2403	0.0216	0.6732	0.6413	1.0491	-0.0718	-0.0871	-0.0788	0.1088	0.0493	0.0322	0.1117	-0.0607	0.0225	0.0453	0.0338	0.0323	0.0804	0.0259	0.0305	0.8821	2.2042	10.1219
4	0.472	-0.0819	0.0366	0.4926	0.0891	0.2242	0.0218	0.0401	-0.0431	0.0117	-0.0309	-0.0221	-0.0142	0.0114	0.0091	0.0241	0.0041	0.005	0.0065	-0.0014	0.0431	34.7493	9.3547	-12.1456
5	2.4601	-1.0515	-0.2789	1.0581	0.1974	0.3219	0.0281	0.0729	-0.2332	-0.0011	-0.0603	0.0671	0.0086	-0.1023	0.0322	0.0046	-0.0019	-0.0111	0.033	-0.0112	0.0472	9.0057	-2.2828	-6.236
6	1.3375	-0.8219	-0.6285	1.224	0.9991	1.414	0.0081	-0.0166	-0.0732	-0.1186	0.0478	0.0473	-0.1952	-0.0042	-0.0559	0.0373	0.0063	0.0085	0.0121	0.0014	0.0245	5.2988	6.0857	-5.1482
7	1.4135	-0.2231	-0.7192	0.3821	0.0489	0.7296	0.0382	0.1697	-0.1757	-0.0361	-0.1101	0.0438	-0.0619	-0.1243	0.0719	0.0141	0.0106	0.0015	0.0669	-0.0352	0.0315	-15.5694	-11.6525	-51.4717
8	0.7832	-0.2537	-0.4674	0.4651	0.1827	0.3085	0.0941	0.1391	0.0297	-0.0587	-0.0709	-0.0191	-0.0721	-0.0933	-0.0232	0.0367	0.0461	0.0053	0.062	0.0056	0.0022	-18.5194	-0.4781	-48.6101
9	1.5631	-0.2928	-0.883	0.144	0.2205	0.7624	0.0255	0.0934	-0.0647	-0.038	-0.0518	-0.0032	-0.0448	-0.0892	0.0263	0.0219	0.0196	0.0104	0.0392	-0.0065	0.0172	-15.8811	-5.2593	-44.6397
10	2.0476	-0.7938	0.2668	0.8108	0.1906	0.4721	0.1067	0.1088	0.0144	-0.0776	-0.0291	0.0111	0.0168	0.0779	-0.0777	0.0435	0.0047	0.0077	0.047	-0.0259	0.0391	2.0214	-13.6029	-50.7976
11	0.2097	-0.1188	0.0987	0.6811	0.0581	3.1802	0.0727	0.0321	0.0132	0.0881	0.0843	-0.1817	-0.0289	0.2323	-0.157	0.0535	0.0164	-0.0269	0.0883	-0.0415	0.0569	19.2855	-16.0386	-26.2242
12	0.3594	0.0498	0.6444	0.7709	-0.1959	1.6027	0.0699	0.038	-0.0828	-0.031	0.0269	-0.0668	0.1246	0.0683	-0.0968	0.0184	0.0118	-0.0165	0.0451	-0.0342	0.0419	10.6506	-21.0356	-38.7052
13	0.1959	-0.3178	0.0781	2.187	-0.398	1.5755	0.0511	0.0537	-0.064	0.0912	-0.0637	0.0204	0.2005	-0.0463	0.0126	0.0603	0.0055	-0.0197	0.022	-0.0224	0.0498	10.059	-26.5695	-31.3262
14	0.7991	-0.9445	1.212	1.8383	-2.6265	3.8219	-0.1154	-0.0754	0.0689	0.1745	0.0006	-0.0938	-0.2455	0.0593	0.1148	0.0495	-0.0058	0.0037	0.0584	-0.0379	0.0346	5.1076	-8.2546	-45.5734
15	0.2689	0.0768	0.3043	1.1058	-0.0333	2.5544	0.1017	0.0346	-0.0853	0.0671	0.0017	-0.1781	0.3059	0.1622	-0.1034	0.0587	0.0331	-0.0454	0.0553	-0.0379	0.0655	17.917	-25.046	-32.6025
16	0.5985	-0.1642	0.1156	1.185	-0.4293	0.898	0.0047	-0.0178	0.0208	0.0471	-0.0461	-0.1341	-0.0633	0.0613	0.0415	0.0265	-0.0047	0.0172	0.0215	0.0069	0.0381	-12.0256	0.3315	-21.5018
17	0.4323	-0.235	-0.1458	0.2844	0.1556	0.8133	0.0664	0.0616	-0.0074	-0.0199	-0.0727	0.0073	-0.0127	-0.0508	0.0063	0.0245	0.0129	0.0193	0.0325	0.0077	0.0332	-21.1419	2.2801	-30.4226
18	1.4262	-0.9745	1.2367	2.2248	-2.2433	2.3596	0.1208	-0.1032	-0.1558	-0.046	0.0833	0.2434	0.1032	-0.1031	-0.2042	0.0431	-0.0198	0.0358	0.0411	0.0093	0.0968	-27.1144	-7.8148	-23.5302
19	0.3454	-0.2203	-0.1945	0.2614	0.1082	0.4127	0.051	0.0043	0.0266	-0.0204	-0.0451	0.0028	-0.0218	0.0076	-0.0059	0.0238	0.0088	0.0231	0.0256	0.0098	0.0349	-18.1978	3.5455	-28.476
20	1.3229	-0.0843	-0.3312	0.3793	0.0095	0.5153	0.0291	-0.1438	-0.001	0.0682	0.048	-0.0251	-0.0083	0.1044	-0.0771	0.0224	0.0009	-0.0033	0.0425	-0.0115	0.0178	7.8708	-10.0686	-21.3521
21	0.7357	0.0782	-0.3824	0.3857	-0.1553	0.8457	0.0077	-0.0047	-0.0083	0.0016	0.0128	-0.0161	-0.002	0.0655	-0.0205	0.0132	-0.0132	0.0089	0.0457	-0.0171	0.0092	11.5283	-5.357	-28.2685
22	0.353	-0.3413	0.0053	4.3005	-0.4976	1.4256	-0.0254	0.1339	0.0817	-0.0245	-0.0216	-0.1779	-0.0855	0.1935	0.047	0.0086	-0.0248	-0.007	0.0877	0.0169	0.1042	50.052	22.2805	-10.3433
23	0.6717	0.3402	-0.4045	2.07	-2.2712	3.0604	0.0384	0.0511	0.0211	-0.03	-0.0158	0.0948	-0.0454	-0.159	-0.0226	0.0204	0.046	-0.0066	0.1097	-0.0104	0.0204	-34.7344	6.6044	-39.1739

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 101
2	X-RAY DIFFRACTION	2	A	102 - 113
3	X-RAY DIFFRACTION	3	A	114 - 214
4	X-RAY DIFFRACTION	4	B	1 - 109
5	X-RAY DIFFRACTION	5	B	110 - 134
6	X-RAY DIFFRACTION	6	B	135 - 216
7	X-RAY DIFFRACTION	7	L	1 - 25
8	X-RAY DIFFRACTION	8	L	26 - 75
9	X-RAY DIFFRACTION	9	L	76 - 101
10	X-RAY DIFFRACTION	10	L	102 - 113
11	X-RAY DIFFRACTION	11	L	114 - 128
12	X-RAY DIFFRACTION	12	L	129 - 150
13	X-RAY DIFFRACTION	13	L	151 - 163
14	X-RAY DIFFRACTION	14	L	164 - 174
15	X-RAY DIFFRACTION	15	L	175 - 214
16	X-RAY DIFFRACTION	16	H	1 - 17
17	X-RAY DIFFRACTION	17	H	18 - 60
18	X-RAY DIFFRACTION	18	H	61 - 66
19	X-RAY DIFFRACTION	19	H	67 - 109
20	X-RAY DIFFRACTION	20	H	110 - 134
21	X-RAY DIFFRACTION	21	H	135 - 216
22	X-RAY DIFFRACTION	22	Z	412 - 423
23	X-RAY DIFFRACTION	23	Y	412 - 423

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Movie

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Structure viewers

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Validation report

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Assembly

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Data collection

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About Yorodumi

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

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Yorodumi