PDB-5o05: GII.10 Vietnam 026 norovirus protruding domain in complex with Na...

ID or keywords:

Entry

Database: PDB / ID: 5o05

Title

GII.10 Vietnam 026 norovirus protruding domain in complex with Nanobody Nano-42

Components

Capsid protein
Nanobody (VHH) Nano-42

Keywords

VIRAL PROTEIN / Norovirus / Protruding domain / capsid protein / Nanobody / VHH

Function / homology

Function and homology information

virion component / host cell cytoplasm
Similarity search - Function

Biological species

Vicugna pacos (alpaca)

Norwalk virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2 Å

Authors

Koromyslova, A.D. / Hansman, G.S.

Citation

Journal: PLoS Pathog. / Year: 2017
Title: Nanobodies targeting norovirus capsid reveal functional epitopes and potential mechanisms of neutralization.
Authors: Koromyslova, A.D. / Hansman, G.S.

History

Deposition	May 16, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 4, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Apr 10, 2019	Group: Data collection / Source and taxonomy / Category: entity_src_gen Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant
Revision 1.3	Jan 17, 2024	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	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	5o05_validation.pdf.gz	475.1 KB	Display	wwPDB validaton report
Full document	5o05_full_validation.pdf.gz	485.4 KB	Display
Data in XML	5o05_validation.xml.gz	35.7 KB	Display
Data in CIF	5o05_validation.cif.gz	51.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o0/5o05 ftp://data.pdbj.org/pub/pdb/validation_reports/o0/5o05	HTTPS FTP

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Related structure data

Related structure data	5o02C 5o03C 5o04C 5ommC 5omnC 3onuS 4x4cS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4x7c-d 4x7e-d 4x7d-d 7433 3wfq-4 7k84-d 1t2k-d 3wfq-3 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	#136 - Apr 2011 Nanobodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (4)

Deposited unit

C: Nanobody (VHH) Nano-42

D: Nanobody (VHH) Nano-42

A: Capsid protein

B: Capsid protein

hetero molecules

97.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software
Evidence: isothermal titration calorimetry

Unit cell

Length a, b, c (Å)	87.930, 105.360, 107.750
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	Nanobody (VHH) Nano-42 Mass: 13189.652 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pHEN6C / Production host: Escherichia coli (E. coli) / Variant (production host): WK6
#2: Protein	Capsid protein Mass: 34506.660 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Norwalk virus / Variant: Vietnam 026 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5F4T5
#3: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.62 Å³/Da / Density % sol: 52.98 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M potassium iodide, 20% (w/v) PEG3350

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID23-2 / Wavelength: 0.8729 Å

Detector

Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 9, 2016

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.8729 Å / Relative weight: 1

Reflection

Resolution: 2→47.327 Å / Num. obs: 68217 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.497 % / B_iso Wilson estimate: 28.38 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.09 / R_rim(I) all: 0.102 / Χ²: 1.051 / Net I/σ(I): 13.08

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2-2.12	4.646	0.742	2.15	10775	0.749	0.838	98.8
2.12-2.27	4.623	0.499	3.16	10276	0.853	0.564	99.9
2.27-2.45	4.501	0.32	4.64	9603	0.923	0.363	99.9
2.45-2.68	4.332	0.204	6.86	8800	0.967	0.232	99.5
2.68-2.99	4.407	0.122	10.93	8013	0.988	0.139	99.9
2.99-3.46	4.658	0.073	18.9	7108	0.996	0.082	99.9
3.46-4.23	4.511	0.04	31.37	6092	0.998	0.046	100
4.23-5.95	4.138	0.029	39.81	4755	0.999	0.033	99.5
5.95-47.327	4.392	0.025	45.98	2795	0.999	0.028	99.1

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	7.33 Å	48.01 Å
Translation	7.33 Å	48.01 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XSCALE		data scaling
PHASER	2.5.6	phasing
PDB_EXTRACT	3.22	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3ONU and 4X4C

3onu

4x4c

Resolution: 2→47.327 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.26

	R_factor	Num. reflection	% reflection
R_free	0.2215	3409	5 %
R_work	0.1799	-	-
obs	0.182	68128	99.68 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2→47.327 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6399	0	156	414	6969

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	6720
X-RAY DIFFRACTION	f_angle_d	1.082	9124
X-RAY DIFFRACTION	f_dihedral_angle_d	12.386	2350
X-RAY DIFFRACTION	f_chiral_restr	0.053	1019
X-RAY DIFFRACTION	f_plane_restr	0.006	1186

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 (%)
1.9989-2.0275	0.3244	136	0.2764	2589	X-RAY DIFFRACTION	97
2.0275-2.0577	0.3376	139	0.2667	2653	X-RAY DIFFRACTION	100
2.0577-2.0899	0.2811	141	0.2537	2669	X-RAY DIFFRACTION	100
2.0899-2.1242	0.2915	140	0.2386	2677	X-RAY DIFFRACTION	100
2.1242-2.1608	0.2635	140	0.2351	2656	X-RAY DIFFRACTION	100
2.1608-2.2001	0.2703	142	0.2257	2689	X-RAY DIFFRACTION	100
2.2001-2.2424	0.2659	142	0.2275	2683	X-RAY DIFFRACTION	100
2.2424-2.2882	0.2627	140	0.2157	2670	X-RAY DIFFRACTION	100
2.2882-2.3379	0.2396	139	0.2041	2648	X-RAY DIFFRACTION	100
2.3379-2.3923	0.2159	143	0.2034	2714	X-RAY DIFFRACTION	100
2.3923-2.4521	0.2433	142	0.1975	2677	X-RAY DIFFRACTION	100
2.4521-2.5184	0.243	139	0.1908	2653	X-RAY DIFFRACTION	99
2.5184-2.5925	0.2223	141	0.1872	2667	X-RAY DIFFRACTION	100
2.5925-2.6762	0.2152	141	0.1814	2690	X-RAY DIFFRACTION	100
2.6762-2.7718	0.2209	143	0.1822	2703	X-RAY DIFFRACTION	100
2.7718-2.8828	0.2176	141	0.1875	2677	X-RAY DIFFRACTION	100
2.8828-3.014	0.225	143	0.177	2725	X-RAY DIFFRACTION	100
3.014-3.1729	0.2353	143	0.176	2701	X-RAY DIFFRACTION	100
3.1729-3.3716	0.2297	142	0.1748	2709	X-RAY DIFFRACTION	100
3.3716-3.6318	0.1896	144	0.1674	2727	X-RAY DIFFRACTION	100
3.6318-3.9971	0.1841	144	0.1517	2737	X-RAY DIFFRACTION	100
3.9971-4.5751	0.1847	145	0.137	2743	X-RAY DIFFRACTION	100
4.5751-5.7626	0.1894	146	0.1465	2767	X-RAY DIFFRACTION	100
5.7626-47.3397	0.2263	153	0.1813	2895	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	5.6208	-1.5957	0.7085	9.694	-6.936	5.0056	0.4468	-0.8178	-0.7017	-0.3805	-0.5387	-0.2736	1.3401	0.0557	0.0693	0.4089	-0.0556	0.0979	0.6241	0.4905	0.8564	-32.0704	-51.1788	42.6879
2	0.4328	0.5475	-0.4638	1.1774	-0.5843	0.5253	0.3382	-1.1252	-0.4634	0.4874	-0.7665	-0.391	0.2291	-0.0197	0.3625	0.5329	-0.2429	-0.0772	0.8729	0.2129	0.4209	-32.2801	-41.1316	50.2772
3	1.098	-1.3087	0.602	1.5671	-0.7775	3.5911	0.6964	-0.5277	1.3517	0.9007	-0.4117	-0.4327	-0.308	0.3613	-0.2595	0.796	-0.481	-0.0291	1.602	0.2468	0.8022	-32.3748	-31.5442	59.1887
4	0.0839	0.2996	0.7213	1.4404	1.9198	7.606	0.3868	-1.0628	-0.9546	0.2034	-0.3747	-0.4852	0.4425	0.5557	-0.0303	0.3715	-0.1236	-0.1458	1.2407	0.3937	0.7239	-24.922	-42.2805	51.6715
5	2.8792	1.0888	-0.9203	2.225	-2.2328	6.8016	0.1755	-1.0609	-0.3336	0.1469	-0.2135	-0.1951	0.0568	-0.1787	0.0147	0.3429	-0.0977	0.0218	0.5623	0.1903	0.4481	-35.4603	-43.0301	47.5241
6	3.9499	-1.8638	2.695	4.9147	-3.7017	3.3103	0.5956	0.5696	-1.1845	-0.8716	0.1122	0.1931	2.4938	0.0211	-0.6427	0.7396	-0.0537	-0.0702	0.6648	-0.3591	0.9286	-23.64	-51.8103	-18.5158
7	2.9565	-4.4187	-2.4199	8.7359	0.1687	7.6632	1.1788	0.9045	0.0805	-1.5427	-1.466	-0.2607	1.852	1.0377	0.251	0.9431	0.0867	-0.0581	1.2082	0.0694	0.4557	-21.1463	-45.5601	-41.2891
8	5.7736	-2.6035	1.1455	6.6397	-1.1261	8.4916	1.2539	1.1651	-0.8134	-0.3911	-0.1701	1.1758	0.6871	-1.2209	-1.1327	0.3795	0.0326	-0.1137	0.7154	-0.2095	0.8414	-26.7346	-46.9083	-25.9029
9	5.8169	-3.4017	0.7417	6.2662	0.9282	0.5364	0.3222	1.1202	-0.5481	0.1932	-0.6548	0.9164	0.4019	-0.1564	0.293	0.3242	-0.0273	-0.0516	0.5131	-0.1966	0.5395	-21.4887	-42.1502	-18.8656
10	4.5709	2.5541	-6.4223	1.9311	-3.6003	9.0455	-0.1796	0.7108	1.0173	-0.2913	0.4413	0.2904	0.2207	-1.3861	-0.2443	0.4812	0.1991	0.0018	0.8638	0.0442	0.4881	-6.0869	-43.5699	-28.1216
11	2.538	-2.5553	1.7476	5.9799	3.1653	8.3436	0.3355	1.5062	-0.0213	-0.9855	-0.8169	0.1806	-0.0299	0.0756	0.4391	0.4427	0.2	-0.0308	0.7103	-0.0512	0.3208	-22.0309	-34.9095	-26.0802
12	2.9325	-0.8454	2.2921	5.5977	-1.182	1.8507	0.374	1.6195	0.5058	-0.6245	-0.3771	0.4123	-0.3685	-0.8451	0.0812	0.5962	0.2784	-0.1165	1.1214	-0.1288	0.4779	-21.6634	-40.9554	-34.3074
13	3.3856	-1.3395	2.271	4.5477	0.1537	1.8044	-0.0407	1.3714	-0.7276	0.201	-0.4443	0.5739	1.0217	0.229	0.5434	0.4139	0.042	0.0126	0.6237	-0.2686	0.4437	-18.3765	-45.1295	-21.1236
14	9.5809	-3.2438	-5.8357	2.3934	4.8028	9.7119	-0.3625	-0.2524	-1.191	-0.2007	0.1107	-0.41	2.0182	0.2376	0.2531	0.587	-0.0013	0.0666	0.2098	-0.0317	0.439	-20.5109	-40.1086	-4.2357
15	3.1808	-0.1893	2.2545	4.6949	-0.2083	8.6008	0.3062	1.1193	-0.3948	0.0587	-0.307	0.3052	1.2307	0.3278	-0.0224	0.3804	0.0974	-0.0165	0.6314	-0.2677	0.6027	-16.7539	-48.5113	-24.05
16	1.8392	-0.5791	0.2362	1.8408	0.5603	2.3364	0.0113	0.1378	-0.1079	-0.0975	-0.0299	-0.0072	0.2438	0.0618	0.0242	0.1854	-0.0147	0.0192	0.1706	-0.0077	0.183	-18.3152	-16.6568	1.4568
17	6.3754	1.7442	1.5679	5.3126	2.6941	1.8724	-0.0356	0.1365	0.4113	-0.1774	0.1574	-0.6135	-0.3505	0.6152	-0.0675	0.2946	-0.0927	-0.0084	0.3734	0.0062	0.2789	-5.8535	4.5498	13.552
18	1.8099	-0.4809	-0.606	1.3648	0.519	2.6853	-0.024	-0.0933	0.2155	0.0516	0.1278	-0.3455	-0.401	0.5606	-0.1006	0.2107	-0.1083	-0.0383	0.2843	-0.0162	0.2653	-7.2416	1.0535	13.8891
19	1.2326	-0.0694	0.4025	1.9223	0.1944	2.2829	0.061	0.1884	0.0483	-0.2638	0.0071	-0.3461	-0.1324	0.3517	-0.0615	0.1985	-0.0472	0.0637	0.2506	0.0055	0.2095	-12.3825	-5.1444	-1.6428
20	1.9657	0.2326	0.2604	4.3389	1.4222	4.3762	-0.0376	0.176	-0.1122	-0.1112	-0.0692	0.3183	0.2391	-0.1101	0.0912	0.2151	-0.0255	0.0226	0.1632	-0.0259	0.1927	-23.6173	-24.257	-3.8972
21	1.2662	-0.1418	-0.2152	1.6447	-0.7214	2.4234	-0.0375	0.0794	0.035	-0.023	0.0388	0.0848	-0.0898	-0.2611	0.0043	0.1515	-0.0124	0.0178	0.165	-0.0135	0.1546	-32.8906	-7.2697	18.5312
22	1.0051	0.0779	-0.1738	1.21	-0.5461	2.503	0.022	0.0001	0.1347	0.1759	0.0259	0.1035	-0.335	-0.1557	-0.0499	0.2261	0.0135	0.0028	0.1718	-0.011	0.2086	-31.7216	2.1855	19.8456
23	1.9747	0.7727	0.0552	4.0822	-0.5885	3.7572	0.0344	-0.2155	-0.219	0.0785	-0.1381	-0.302	0.289	0.1368	0.0849	0.2094	0.001	0.0196	0.1739	0.0337	0.2232	-25.03	-24.1146	29.6514

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 1 through 7 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 8 through 59 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 60 through 66 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 67 through 82 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 83 through 118 )
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 1 through 7 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 8 through 17 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 18 through 26 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 27 through 39 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 40 through 45 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 46 through 76 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 77 through 90 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 91 through 99 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 100 through 106 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 107 through 118 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 224 through 279 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 280 through 307 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 308 through 390 )
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 391 through 455 )
20	X-RAY DIFFRACTION	20	chain 'A' and (resid 456 through 538 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 224 through 327 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 328 through 455 )
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 456 through 538 )

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-Yorodumi

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Movie

-
Structure viewers

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Viewer log

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This page

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This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

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Downloads & links

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Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Phasing

-
Processing

+
About Yorodumi

-
News

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

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Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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Yorodumi