PDB-8pmz: HEV gt3 P domain in complex with glycan-insensitive nAb p61.15

ID or keywords:

Entry

Database: PDB / ID: 8pmz

Title

HEV gt3 P domain in complex with glycan-insensitive nAb p61.15

Components

Pro-secreted protein ORF2
scFv_p61.15

Keywords

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

Function / homology

Function and homology information

T=1 icosahedral viral capsid / host cell endoplasmic reticulum / host cell Golgi apparatus / host cell surface / structural molecule activity / RNA binding / extracellular region
Similarity search - Function

Biological species

Paslahepevirus balayani

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.912 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	8pmz.cif.gz	308.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8pmz.ent.gz	250.4 KB	Display	PDB format
PDBx/mmJSON format	8pmz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8pmz_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	8pmz_full_validation.pdf.gz	1 MB	Display
Data in XML	8pmz_validation.xml.gz	30 KB	Display
Data in CIF	8pmz_validation.cif.gz	43.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pm/8pmz ftp://data.pdbj.org/pub/pdb/validation_reports/pm/8pmz	HTTPS FTP

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Related structure data

Related structure data	8pmwC 8pmxC 8pmyC 8pn0C 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	#256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (1)

Deposited unit

A: Pro-secreted protein ORF2

B: scFv_p61.15

C: Pro-secreted protein ORF2

D: scFv_p61.15

hetero molecules

101 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)	108.59, 178.77, 49.66
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	B-364- HOH

#1: Protein	Pro-secreted protein ORF2 / pORF2 / Protein ORF2 Mass: 22868.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paslahepevirus balayani / Plasmid: pMT / Cell line (production host): Schneider 2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: C4B4T9
#2: Antibody	scFv_p61.15 Mass: 27160.129 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 2 cells / Production host: Drosophila melanogaster (fruit fly)
#3: Chemical	ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₂₆N₂O₆ / Comment: pH buffer*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H₂O
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: 48.94 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% w/v PEG 3350, 0.1M Bis-Tris propane pH 8.5 and 0.2M Potassium thiocyanate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99987 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 6, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99987 Å / Relative weight: 1
Reflection	Resolution: 1.912→47.85 Å / Num. obs: 74611 / % possible obs: 97.1 % / Redundancy: 13.52 % / CC_1/2: 0.997 / R_rim(I) all: 0.176 / Net I/σ(I): 11.23
Reflection shell	Resolution: 1.912→1.98 Å / Num. unique obs: 5776 / CC_1/2: 0.906

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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: 1.912→47.85 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.921 / SU R Cruickshank DPI: 0.156 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.158 / SU R_free Blow DPI: 0.145 / SU R_free Cruickshank DPI: 0.145

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2565	3634	-	RANDOM
R_work	0.2246	-	-	-
obs	0.2262	72647	95.8 %	-

Displacement parameters

B_iso mean: 36.26 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.511 Å²	0 Å²	0 Å²
2-	-	-1.3156 Å²	0 Å²
3-	-	-	1.8266 Å²

Refine analyze

Luzzati coordinate error obs: 0.28 Å

Refinement step

Cycle: LAST / Resolution: 1.912→47.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5804	0	38	321	6163

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.008	5992	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	0.98	8181	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		1943	SINUSOIDAL	2
X-RAY DIFFRACTION	t_gen_planes		990	HARMONIC	5
X-RAY DIFFRACTION	t_it		5992	HARMONIC	10
X-RAY DIFFRACTION	t_chiral_improper_torsion		801	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_ideal_dist_contact		4987	SEMIHARMONIC	4
X-RAY DIFFRACTION	t_omega_torsion	3.9
X-RAY DIFFRACTION	t_other_torsion	14.39

LS refinement shell

Resolution: 1.912→1.93 Å

	R_factor	Num. reflection	% reflection
R_free	0.5931	73	-
R_work	0.5745	-	-
obs	-	-	56.63 %

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	9.643	5.5541	-1.6114	9.9959	1.0289	4.4693	0.1764	0.594	0.3238	0.594	-0.0841	0.3244	0.3238	0.3244	-0.0923	-0.0285	0.0226	-0.0292	0.0273	0.0022	0.0141	-17.2846	10.4316	9.4798
2	0.3372	-0.1816	0.0073	0.5638	-0.48	0.0051	0.0168	0.0836	0.0409	0.0836	0.0138	0.001	0.0409	0.001	-0.0306	-0.0349	-0.035	0.015	0.0528	-0.0196	0.0797	-28.3177	25.618	6.3792
3	0.3098	-1.0508	0.0262	0.8699	-0.8094	0.6974	0.0841	0.1495	0.0816	0.1495	0.0046	-0.1009	0.0816	-0.1009	-0.0887	-0.0053	-0.0418	-0.0043	0.0682	0.0168	0.0217	-23.7902	16.1876	16.2323
4	0.657	-0.0678	-0.3497	0.2489	0.0337	0.4696	0.0171	0.0628	0.021	0.0628	-0.0298	-0.0496	0.021	-0.0496	0.0127	-0.0345	-0.0329	0.0088	0.0646	-0.0135	0.058	-24.3698	29.8862	7.1894
5	6.1215	-1.9808	0.7086	1.0239	-0.5369	1.9214	0.0509	0.0827	0.0923	0.0827	-0.112	0.248	0.0923	0.248	0.0612	-0.0342	-0.0508	-0.0082	-0.0302	0.0107	0.0514	-22.4359	23.7469	5.2184
6	2.1511	-0.1121	1.5633	1.3329	-0.3573	1.8264	-0.0649	-0.1542	-0.1257	-0.1542	-0.0296	-0.0608	-0.1257	-0.0608	0.0945	-0.0306	0.0368	-0.0456	-0.0241	-0.0391	0.123	-56.9007	34.2081	0.2049
7	2.7992	-1.4002	0.1585	3.1544	-0.4833	0.8833	0.0237	-0.553	-0.0495	-0.553	-0.0692	0.0014	-0.0495	0.0014	0.0455	-0.0289	0.0123	-0.0125	-0.0045	-0.0005	0.0279	-50.0035	29.5944	-5.9042
8	1.5047	-0.106	0.439	1.434	-0.9522	0.4333	-0.0047	-0.0728	0.0567	-0.0728	-0.0153	-0.082	0.0567	-0.082	0.02	-0.05	0.0242	-0.0182	-0.0088	-0.044	0.1061	-54.6443	28.9366	-1.2356
9	1.7412	1.3065	0.1643	1.6707	-0.3107	0.2435	0.041	0.0527	-0.0103	0.0527	-0.0252	0.0022	-0.0103	0.0022	-0.0159	-0.0775	-0.0305	0.032	0.0185	-0.0169	0.1116	-53.9342	11.0677	7.7398
10	4.0828	5.3363	-2.5444	7.1942	-3.4998	1.7655	0.0151	0.1102	-0.0653	0.1102	0.1937	-0.0277	-0.0653	-0.0277	-0.2088	-0.0927	-0.0452	-0.0125	-0.0141	0.0035	0.1611	-57.4266	11.7414	0.2887
11	12.6016	-5.8208	-3.0429	3.1143	2.0135	3.9163	0.1482	-0.0718	0.0324	-0.0718	0.0821	0.1789	0.0324	0.1789	-0.2303	-0.0143	-0.0515	-0.0091	0.0412	-0.0192	0.0113	-17.0451	12.1742	-13.7568
12	0.4888	0.4968	0.1163	0	0.2885	0.5109	-0.0342	0.0157	0.0339	0.0157	0.0731	0.0314	0.0339	0.0314	-0.0389	-0.051	-0.0022	0.0256	0.0597	0	0.0806	-5.8987	26.7278	-8.763
13	1.1546	1.9772	0.1457	0.4357	0.6105	0.4228	0.0295	-0.2144	0.0097	-0.2144	0.0916	0.069	0.0097	0.069	-0.1211	-0.0064	-0.018	0.0397	0.0865	-0.0234	0.0119	-10.5839	18.8047	-19.8909
14	0.4719	0.261	-0.2955	0.5229	0.105	0.5507	0.0094	-0.0551	0.0065	-0.0551	0.0097	-0.0051	0.0065	-0.0051	-0.0191	-0.0507	-0.0252	0.0225	0.073	0.0046	0.0619	-9.8637	30.1537	-8.3672
15	2.5772	1.304	3.1246	0.4052	-4.7141	0	-0.1274	-0.0197	-0.4521	-0.0197	-0.2281	0.0156	-0.4521	0.0156	0.3555	0.1893	0.0284	0.0189	0.0881	-0.0128	-0.0321	-20.9019	28.3233	-23.7461
16	5.3786	0.0023	1.5465	0.6984	1.4393	0.3035	-0.0296	-0.0338	0.0981	-0.0338	-0.1477	0.5966	0.0981	0.5966	0.1773	-0.209	-0.0606	-0.0906	-0.015	0.0683	0.239	26.1458	34.8286	-0.3738
17	2.3062	0.068	-0.6325	1.134	0.7385	0.5196	-0.0072	0.2968	-0.1778	0.2968	0.0705	0.0982	-0.1778	0.0982	-0.0633	-0.1502	-0.0405	-0.0641	0.0158	0.0401	0.1975	18.95	26.6751	-1.7965
18	5.009	2.1526	-2.0814	1.1192	-4.1993	11.1854	0.0829	0.1967	0.1918	0.1967	-0.1766	-0.4117	0.1918	-0.4117	0.0936	-0.1211	-0.1043	0.0012	0.0349	0.0282	0.0921	10.7501	31.8619	1.6934
19	4.0723	2.848	-2.1503	8.0278	-4.7709	2.7978	-0.0593	0.2167	-0.0428	0.2167	-0.04	-0.1152	-0.0428	-0.1152	0.0992	-0.069	-0.1224	-0.0902	0.0427	0.0286	0.0433	17.75	36.4138	3.5789
20	3.0874	0.9139	1.6506	1.3677	0.8043	1.9478	0.0307	0.0221	0.0936	0.0221	-0.1052	0.0047	0.0936	0.0047	0.0745	-0.1813	-0.0118	0.0008	-0.0486	0.0979	0.2618	20.7127	27.4569	-1.8819
21	9.0264	5.667	5.4164	0.2992	-1.6678	1.4506	-0.0729	0.1741	0.1236	0.1741	0.1054	0.0118	0.1236	0.0118	-0.0324	-0.2047	0.0988	-0.0911	-0.0337	0.1219	0.3035	15.8705	11.3393	-0.1791
22	4.2866	-3.5825	-5.8208	1.6243	0.9777	9.7492	0.2296	-0.0491	0.989	-0.0491	-0.0853	0.2119	0.989	0.2119	-0.1443	-0.1722	0.2399	-0.0099	-0.2107	-0.213	0.6036	24.1714	4.1213	-12.4981
23	0	0.2092	0.1329	1.5578	0.4479	1.8716	0.0493	-0.1741	0.1924	-0.1741	-0.0714	0.147	0.1924	0.147	0.0221	-0.2358	0.0739	0.0575	0.0302	-0.0156	0.3053	18.7096	16.8285	-10.3165
24	3.8184	-1.8612	0.6746	1.0171	1.0076	1.1295	0.338	-0.5606	0.1313	-0.5606	-0.1176	0.3968	0.1313	0.3968	-0.2205	-0.1344	0.093	0.1682	0.1316	-0.1828	0.2575	19.1083	12.8821	-18.5501
25	6.7993	0.1255	1.6653	2.5542	1.2145	0.3207	0.0753	0.1848	-0.0605	0.1848	0.1224	-0.2094	-0.0605	-0.2094	-0.1977	-0.204	0.0143	0.0036	-0.0943	-0.017	0.4059	19.3561	14.9836	-6.9189

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{A\|459 - 468}	A	459 - 468
2	X-RAY DIFFRACTION	2	{A\|469 - 507}	A	469 - 507
3	X-RAY DIFFRACTION	3	{A\|508 - 530}	A	508 - 530
4	X-RAY DIFFRACTION	4	{A\|531 - 590}	A	531 - 590
5	X-RAY DIFFRACTION	5	{A\|591 - 605}	A	591 - 605
6	X-RAY DIFFRACTION	6	{B\|1 - 37}	B	1 - 37
7	X-RAY DIFFRACTION	7	{B\|38 - 74}	B	38 - 74
8	X-RAY DIFFRACTION	8	{B\|75 - 143}	B	75 - 143
9	X-RAY DIFFRACTION	9	{B\|144 - 236}	B	144 - 236
10	X-RAY DIFFRACTION	10	{B\|237 - 250}	B	237 - 250
11	X-RAY DIFFRACTION	11	{C\|459 - 468}	C	459 - 468
12	X-RAY DIFFRACTION	12	{C\|469 - 507}	C	469 - 507
13	X-RAY DIFFRACTION	13	{C\|508 - 530}	C	508 - 530
14	X-RAY DIFFRACTION	14	{C\|531 - 603}	C	531 - 603
15	X-RAY DIFFRACTION	15	{C\|604 - 609}	C	604 - 609
16	X-RAY DIFFRACTION	16	{D\|1 - 28}	D	1 - 28
17	X-RAY DIFFRACTION	17	{D\|29 - 48}	D	29 - 48
18	X-RAY DIFFRACTION	18	{D\|49 - 63}	D	49 - 63
19	X-RAY DIFFRACTION	19	{D\|64 - 81}	D	64 - 81
20	X-RAY DIFFRACTION	20	{D\|82 - 122}	D	82 - 122
21	X-RAY DIFFRACTION	21	{D\|123 - 149}	D	123 - 149
22	X-RAY DIFFRACTION	22	{D\|150 - 168}	D	150 - 168
23	X-RAY DIFFRACTION	23	{D\|169 - 187}	D	169 - 187
24	X-RAY DIFFRACTION	24	{D\|188 - 222}	D	188 - 222
25	X-RAY DIFFRACTION	25	{D\|223 - 248}	D	223 - 248

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