PDB-8pn0: HEV gt3 P domain in complex with glycan-sensitive nAb p60.12

ID or keywords:

Entry

Database: PDB / ID: 8pn0

Title

HEV gt3 P domain in complex with glycan-sensitive nAb p60.12

Components

Capsid protein
Fab_p60.12-HC
Fab_p60.12-LC

Keywords

VIRAL PROTEIN / HEV / P domain / non-glycosylated / glycan-sensitive / neutralizing antibody (nAb)

Function / homology

: / : / Structural protein 2 second domain / Structural protein 2 C-terminal domain / viral capsid / Capsid protein

Function and homology information

Biological species

Homo sapiens (human)

Paslahepevirus balayani

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.072 Å

Authors

Ssebyatika, G. / Krey, T.

Funding support

Germany, 1items

Citation

Journal: To Be Published
Title: A novel class of broadly neutralizing hepatitis E virus-specific human antibodies
Authors: Ssebyatika, G. / Dinkelborg, K. / Stroeh, L.J. / Hinte, F. / Corneillie, L. / Hueffner, L. / Guzman, E.M. / Nankya, P.L. / Plueckebaum, N. / Prallet, S. / Mehnert, A.K. / Verhoye, L. / ...

History

Deposition	Jun 29, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 10, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8pn0.cif.gz	547.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8pn0.ent.gz		Display	PDB format
PDBx/mmJSON format	8pn0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8pn0_validation.pdf.gz	488.3 KB	Display	wwPDB validaton report
Full document	8pn0_full_validation.pdf.gz	503.2 KB	Display
Data in XML	8pn0_validation.xml.gz	49.5 KB	Display
Data in CIF	8pn0_validation.cif.gz	69.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pn/8pn0 ftp://data.pdbj.org/pub/pdb/validation_reports/pn/8pn0	HTTPS FTP

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Related structure data

Related structure data	8pmwC 8pmxC 8pmyC 8pmzC C: citing same article (ref.)
Similar structure data	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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Fab_p60.12-HC

B: Fab_p60.12-LC

C: Capsid protein

D: Capsid protein

E: Capsid protein

F: Capsid protein

H: Fab_p60.12-HC

L: Fab_p60.12-LC

187 kDa, 8 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)	88.43, 94.48, 91.25
Angle α, β, γ (deg.)	90, 90.21, 90
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Fab_p60.12-HC Mass: 24858.822 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMT / Cell line (production host): Schneider S2 cells / Production host: Drosophila melanogaster (fruit fly)
#2: Antibody	Fab_p60.12-LC Mass: 22903.221 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMT / Cell line (production host): Schneider's S2 cells / Production host: Drosophila melanogaster (fruit fly)
#3: Protein	Capsid protein Mass: 22868.492 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paslahepevirus balayani / Plasmid: pMT / Cell line (production host): Schneider's S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A6C0PR31
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.04 Å³/Da / Density % sol: 39.66 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 25% w/v PEG 4000, 0.2M Calcium chloride and 0.1M Tris pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999987 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.999987 Å / Relative weight: 1
Reflection	Resolution: 2.072→47.24 Å / Num. obs: 77331 / % possible obs: 84.75 % / Redundancy: 3.27 % / CC_1/2: 0.991 / R_rim(I) all: 0.129 / Net I/σ(I): 5.3
Reflection shell	Resolution: 2.072→2.146 Å / Num. unique obs: 3527 / CC_1/2: 0.193

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Processing

Software

Name	Version	Classification
BUSTER	2.10.4	refinement
XDS		data reduction
pointless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.072→47.24 Å / Cor.coef. F_o:F_c: 0.938 / Cor.coef. F_o:F_c free: 0.914 / SU R Cruickshank DPI: 0.288 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.272 / SU R_free Blow DPI: 0.209 / SU R_free Cruickshank DPI: 0.217

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2608	3868	-	RANDOM
R_work	0.2259	-	-	-
obs	0.2276	77331	84.8 %	-

Displacement parameters

B_iso mean: 50.21 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.0643 Å²	0 Å²	-0.0053 Å²
2-	-	-4.5545 Å²	0 Å²
3-	-	-	3.4902 Å²

Refine analyze

Luzzati coordinate error obs: 0.32 Å

Refinement step

Cycle: LAST / Resolution: 2.072→47.24 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10963	0	0	184	11147

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.008	11236	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.01	15379	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		3584	SINUSOIDAL	2
X-RAY DIFFRACTION	t_gen_planes		1859	HARMONIC	5
X-RAY DIFFRACTION	t_it		11236	HARMONIC	10
X-RAY DIFFRACTION	t_chiral_improper_torsion		1560	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_ideal_dist_contact		8274	SEMIHARMONIC	4
X-RAY DIFFRACTION	t_omega_torsion	3.79
X-RAY DIFFRACTION	t_other_torsion	15.09

LS refinement shell

Resolution: 2.072→2.11 Å

	R_factor	Num. reflection	% reflection
R_free	0.3754	78	-
R_work	0.3892	-	-
obs	-	-	31.62 %

Refinement TLS params.

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	0.0081	0.5781	-0.791	1.2932	0.8409	0.0025	0.0419	0.0873	-0.3875	0.0873	-0.1057	0.284	-0.3875	0.284	0.0638	-0.039	-0.0526	0.0252	0.0368	0.0386	-0.0365	27.1466	21.6587	21.5126
2	1.1145	-0.3396	0.3254	0	-0.7159	0.4402	0.0868	-0.0199	-0.0768	-0.0199	-0.1092	0.1326	-0.0768	0.1326	0.0224	-0.0115	-0.0165	0.0101	0.0533	0.0068	-0.0696	21.8682	15.5841	19.0406
3	0.7598	-1.5289	2.1428	0	-0.9602	2.1646	-0.0386	0.1301	0.3723	0.1301	0.4188	-0.1096	0.3723	-0.1096	-0.3802	-0.0787	-0.0803	0.0387	0.2846	0.1517	-0.2221	53.6471	10.1159	3.7651
4	3.6822	-0.653	-0.7613	0	-1.0549	3.1556	0.0497	0.3594	0.2388	0.3594	0.2375	0.1578	0.2388	0.1578	-0.2872	-0.1538	-0.0411	-0.0324	0.1805	0.0637	-0.1346	57.1486	9.9032	2.5627
5	-0.0038	-0.3406	0.5162	0	-0.5912	1.6548	0.2093	0.1009	0.2224	0.1009	-0.1428	0.186	0.2224	0.186	-0.0666	-0.0012	0.0703	0.0043	0.0556	0.0034	-0.0861	14.4805	12.1951	-0.6886
6	0.0037	-1.2468	-0.5016	0	0.2183	1.0323	0.3616	0.042	0.2267	0.042	-0.1814	0.2707	0.2267	0.2707	-0.1802	-0.0137	0.1511	-0.0312	0.1509	-0.0111	-0.1262	25.468	9.0938	-2.5933
7	2.3939	-0.8007	1.8218	0.2143	-1.4197	2.8755	0.1156	0.2932	-0.2279	0.2932	0.3174	-0.145	-0.2279	-0.145	-0.4331	-0.1592	0.0685	-0.1522	0.1152	0.1522	-0.0924	45.5836	-0.7304	-1.2558
8	0.9107	1.9555	2.9137	0	1.7251	0.0213	-0.0656	0.1432	0.5441	0.1432	0.0859	0.0509	0.5441	0.0509	-0.0204	-0.0725	0.1518	-0.1524	0.0305	0.0627	0.0403	48.5678	-10.0617	-3.8901
9	0.4095	-0.3686	-0.0192	0.4604	-0.2378	0.4822	-0.0694	0.0369	0.0044	0.0369	0.1085	-0.0741	0.0044	-0.0741	-0.0391	-0.0026	0.0133	0.0163	0.0276	0.1064	-0.0515	-14.0351	29.2917	3.0167
10	1.0353	0.1768	-0.3374	0.0963	-0.0787	0.2482	0.0368	-0.0139	-0.015	-0.0139	0.0165	-0.0237	-0.015	-0.0237	-0.0533	0.0241	-0.0031	0.0036	-0.0291	0.0495	-0.03	-10.463	15.6435	23.02
11	0.1264	0.3548	-0.0632	0	-0.1714	0.9933	-0.1146	-0.012	0.1605	-0.012	0.0804	-0.1651	0.1605	-0.1651	0.0342	0.0316	-0.0406	0.0207	-0.0296	0.008	-0.0279	-17.1864	-28.7555	42.6005
12	0.6358	-0.0284	0.1049	0.2176	-0.2246	0.2334	-0.1187	0.0313	0.0753	0.0313	0.0723	-0.071	0.0753	-0.071	0.0464	-0.0077	-0.0437	0.0175	0.0224	0.0052	-0.0414	-13.7332	-14.8586	22.7127
13	1.115	0.5586	0.6504	0.2242	0.1872	0.5453	-0.0481	0.098	0.0834	0.098	-0.0933	0.0791	0.0834	0.0791	0.1414	-0.0225	0.0131	0.044	-0.0321	0.0009	0.0194	22.7362	-18.5327	26.6127
14	1.0542	0.1072	-0.0686	1.8324	-0.6248	0.066	0.0773	-0.0089	0.085	-0.0089	-0.0153	-0.2392	0.085	-0.2392	-0.062	-0.0135	0.0029	0.0521	0.0215	-0.0005	-0.0473	16.6289	-14.9716	20.6901
15	0.7755	-0.0694	0.0591	0	0.0472	0.0074	-0.0966	-0.0033	0.046	-0.0033	0.0537	0.0854	0.046	0.0854	0.0429	-0.0015	0.0137	0.0302	0.0221	0.0155	-0.0462	32.9436	-11.8412	34.4852
16	0.544	0.4184	0.4784	0.0392	-0.9869	2.4127	-0.1421	0.0377	0.044	0.0377	0.1816	-0.0478	0.044	-0.0478	-0.0395	-0.0619	0.0548	0.0228	0.0517	0.0125	-0.0444	53.187	-10.767	44.6614
17	0.6159	0.2212	0.7711	0.2421	-0.0012	1.1111	-0.0054	-0.0374	-0.0459	-0.0374	-0.0779	-0.0503	-0.0459	-0.0503	0.0833	0.0008	0.0252	0.013	-0.028	-0.0125	-0.0164	11.8755	-12.0996	46.0858
18	0.5793	0.9678	0.3543	0	0.7778	0.0026	-0.0704	0.0595	-0.216	0.0595	0.0179	0.147	-0.216	0.147	0.0525	-0.0097	0.02	0.019	-0.005	0.0004	-0.0098	14.5542	-9.5018	44.9231
19	2.004	0.85	-0.8755	0.0575	-0.584	0.7289	0.0602	0.1185	0.0561	0.1185	-0.0114	-0.0544	0.0561	-0.0544	-0.0488	-0.0477	0.0173	0.062	0.0199	0.0368	0.0062	44.0581	2.0257	49.8942
20	2.5995	0.9669	-2.1237	0.0069	-0.7808	1.9581	0.2258	0.0976	-0.0593	0.0976	0.0906	-0.2403	-0.0593	-0.2403	-0.3164	-0.0806	0.0374	0.0624	-0.0394	0.0644	0.0203	44.057	4.16	49.2203

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{A\|2 - 31}	A	2 - 31
2	X-RAY DIFFRACTION	2	{A\|32 - 121}	A	32 - 121
3	X-RAY DIFFRACTION	3	{A\|122 - 176}	A	122 - 176
4	X-RAY DIFFRACTION	4	{A\|177 - 224}	A	177 - 222
5	X-RAY DIFFRACTION	5	{B\|3 - 76}	B	3 - 76
6	X-RAY DIFFRACTION	6	{B\|77 - 123}	B	77 - 123
7	X-RAY DIFFRACTION	7	{B\|124 - 186}	B	124 - 186
8	X-RAY DIFFRACTION	8	{B\|187 - 216}	B	187 - 215
9	X-RAY DIFFRACTION	9	{E\|459 - 604}	E	459 - 604
10	X-RAY DIFFRACTION	10	{F\|459 - 604}	F	459 - 604
11	X-RAY DIFFRACTION	11	{C\|459 - 604}	C	459 - 604
12	X-RAY DIFFRACTION	12	{D\|459 - 604}	D	459 - 604
13	X-RAY DIFFRACTION	13	{H\|2 - 45}	H	2 - 45
14	X-RAY DIFFRACTION	14	{H\|46 - 83}	H	46 - 83
15	X-RAY DIFFRACTION	15	{H\|84 - 156}	H	84 - 156
16	X-RAY DIFFRACTION	16	{H\|157 - 224}	H	157 - 224
17	X-RAY DIFFRACTION	17	{L\|3 - 68}	L	3 - 68
18	X-RAY DIFFRACTION	18	{L\|69 - 110}	L	69 - 110
19	X-RAY DIFFRACTION	19	{L\|111 - 161}	L	111 - 161
20	X-RAY DIFFRACTION	20	{L\|162 - 216}	L	162 - 215

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