PDB-5omm: GII.10 Vietnam 026 protruding domain in complex with Nanobody Nano-14

ID or keywords:

Entry

Database: PDB / ID: 5omm

Title

GII.10 Vietnam 026 protruding domain in complex with Nanobody Nano-14

Components

Capsid protein
Nanobody (VHH) Nano-14

Keywords

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

Function / homology

Function and homology information

virion component / host cell cytoplasm
Similarity search - Function

Biological species

Norovirus GII.10

Vicugna pacos (alpaca)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.7 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	Aug 1, 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	Nov 13, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5omm.cif.gz	292.7 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	5omm.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/om/5omm ftp://data.pdbj.org/pub/pdb/validation_reports/om/5omm	HTTPS FTP

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Related structure data

Related structure data	5o02C 5o03C 5o04C 5o05C 5omnC C: citing same article (ref.)
Similar structure data	1a02-d 4cj1-d 3mwb-d 6c0e-d 3h9g-2 6kfm-d 3h9q-1 4my0-3 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

A: Capsid protein

B: Capsid protein

C: Nanobody (VHH) Nano-14

hetero molecules

83.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

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

Unit cell

Length a, b, c (Å)	97.512, 94.209, 101.284
Angle α, β, γ (deg.)	90.00, 112.70, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Capsid protein / GII.10 Protruding domain Mass: 34506.660 Da / Num. of mol.: 2 / Fragment: Protruding domain, UNP residues 224-538 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Norovirus GII.10 / Plasmid: pMBP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5F4T5
#2: Antibody	Nanobody (VHH) Nano-14 Mass: 12979.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#3: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 25 Source method: isolated from a genetically manipulated source Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.71 Å³/Da / Density % sol: 54.57 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M sodium citrate, 20% (w/v) PEG3000

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: MASSIF-3 / Wavelength: 0.9677 Å

Detector

Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 23, 2016

Radiation

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

Radiation wavelength

Wavelength: 0.9677 Å / Relative weight: 1

Reflection

Resolution: 1.65→48.497 Å / Num. obs: 99684 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 4.901 % / B_iso Wilson estimate: 16.98 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.064 / R_rim(I) all: 0.072 / Χ²: 1.045 / Net I/σ(I): 16.55 / Num. measured all: 488528

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
1.65-1.75	4.887	0.561	2.78	15617	0.806	0.628	95.3
1.75-1.87	4.988	0.337	4.86	15228	0.93	0.376	99.1
1.87-2.02	4.943	0.204	7.9	14277	0.974	0.229	99.5
2.02-2.21	4.822	0.129	12.09	13104	0.988	0.144	99.4
2.21-2.47	4.476	0.085	16.64	11323	0.993	0.097	94.5
2.47-2.85	4.992	0.062	23.3	10345	0.997	0.069	97.9
2.85-3.49	5.135	0.041	34.72	8964	0.999	0.045	99.8
3.49-4.92	5.057	0.029	47.37	6922	0.999	0.032	99.7
4.92-48.497	4.904	0.027	49.28	3904	0.999	0.03	99.2

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Resolution: 1.7→48.497 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.48 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1929	1836	2.01 %	RANDOM
R_work	0.1656	-	-	-
obs	0.1662	91506	98.68 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.7→48.497 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5374	0	100	417	5891

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5664
X-RAY DIFFRACTION	f_angle_d	1.164	7706
X-RAY DIFFRACTION	f_dihedral_angle_d	11.567	1971
X-RAY DIFFRACTION	f_chiral_restr	0.058	868
X-RAY DIFFRACTION	f_plane_restr	0.006	1005

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 (%)
1.7-1.746	0.2765	142	0.2328	6927	X-RAY DIFFRACTION	99
1.746-1.7974	0.2122	139	0.1912	6829	X-RAY DIFFRACTION	99
1.7974-1.8554	0.217	141	0.175	6884	X-RAY DIFFRACTION	99
1.8554-1.9217	0.2049	143	0.1755	6983	X-RAY DIFFRACTION	100
1.9217-1.9986	0.1957	143	0.1726	6952	X-RAY DIFFRACTION	100
1.9986-2.0896	0.202	142	0.162	6920	X-RAY DIFFRACTION	100
2.0896-2.1998	0.2039	143	0.1667	6971	X-RAY DIFFRACTION	99
2.1998-2.3376	0.2148	140	0.1649	6893	X-RAY DIFFRACTION	99
2.3376-2.5181	0.2013	129	0.1679	6251	X-RAY DIFFRACTION	90
2.5181-2.7714	0.2089	141	0.1738	6942	X-RAY DIFFRACTION	99
2.7714-3.1724	0.1706	144	0.1701	6991	X-RAY DIFFRACTION	100
3.1724-3.9966	0.1754	143	0.1569	7032	X-RAY DIFFRACTION	100
3.9966-48.5167	0.1757	146	0.1489	7095	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	1.9476	-0.0826	0.0696	1.0692	0.1956	1.0223	0.0048	0.0623	-0.0908	0.0097	0.0066	-0.0638	0.0898	0.0102	-0.0041	0.0948	0.0011	-0.002	0.0627	-0.0089	0.1049	29.6629	12.8196	12.0337
2	1.2945	-0.5146	-0.3237	2.0938	0.4916	1.1985	-0.0171	0.0813	-0.0427	-0.0613	-0.0804	0.3655	-0.0689	-0.1954	0.0803	0.0737	-0.0052	-0.0202	0.1255	-0.0152	0.1419	12.5503	17.3456	12.7495
3	1.062	-0.1711	0.0443	0.8888	0.2058	1.1211	-0.027	-0.0135	-0.1943	0.0872	0.0235	-0.0273	0.2255	0.0441	0.0223	0.1092	0.0057	-0.006	0.0751	0.0118	0.1375	29.1864	4.6022	16.8767
4	2.843	0.1431	-0.9673	1.8233	-0.9764	1.9596	-0.032	-0.0769	0.0074	0.1756	0.0139	-0.4237	-0.0326	0.2231	0.0094	0.1001	0.0175	-0.0469	0.1354	-0.0448	0.2102	47.5405	15.0277	16.9722
5	4.5914	-0.8046	2.1573	3.5017	-0.1746	6.8996	0.0662	-0.0132	-0.2841	0.1819	0.0117	-0.3334	0.173	0.5443	-0.0644	0.1242	0.0381	-0.0471	0.1415	-0.0068	0.2445	50.5567	6.8615	18.2293
6	4.7996	-1.7867	-2.3156	3.1664	0.2453	2.4369	-0.1339	-0.4023	-0.13	0.4674	0.2101	-0.4579	0.1702	0.202	-0.0716	0.2173	0.0443	-0.1327	0.2487	-0.0165	0.3003	52.9153	7.0326	22.9647
7	0.9924	0.4397	-0.2807	1.6756	-0.2677	2.0737	0.0327	-0.1263	0.0204	0.2056	-0.0118	-0.0958	-0.0231	-0.0202	-0.02	0.1092	0.0078	-0.0226	0.0987	-0.0138	0.0982	31.3166	31.7295	26.6942
8	1.3757	0.3407	0.179	3.3678	0.1898	1.4034	0.0588	-0.2453	-0.0802	0.4741	-0.1002	0.2756	0.1804	-0.0989	0.0256	0.1734	-0.0174	0.0425	0.1757	-0.0001	0.0943	18.9334	21.9113	34.9081
9	1.1078	0.3689	-0.1624	1.4057	0.0372	0.8295	0.0109	0.0089	0.0709	0.0133	0.0096	-0.1145	-0.1456	0.0666	-0.0185	0.1019	0.0054	-0.0159	0.0961	-0.009	0.1212	33.0712	39.992	16.4517
10	9.0913	-7.2406	-2.6392	6.0371	1.7044	1.6103	-0.7027	1.0819	-0.231	0.2325	-0.1332	0.8453	-0.0523	-2.0762	0.8343	0.4496	-0.0349	0.0536	0.7082	-0.1551	0.5352	-0.7642	18.7314	29.2739
11	0.3413	0.0816	-0.1084	0.0325	-0.0417	0.0571	-0.0838	0.1167	-0.0435	0.5121	-0.069	0.0524	0.0959	-0.2968	0.1426	0.8404	-0.0566	0.2082	0.8999	-0.6799	0.9676	-10.7436	15.9633	43.9122
12	7.5158	-3.4058	-4.6279	2.175	0.2826	8.0579	0.5126	0.5319	0.1984	-0.2318	-0.3235	-0.209	-0.2308	0.2209	-0.172	0.4532	0.0436	0.2515	0.9875	-0.4701	0.8894	-11.9274	12.9102	34.913
13	2.2338	-0.4114	2.9537	6.9477	4.5367	7.7853	-0.2443	-0.6132	0.4678	-0.0286	-0.3689	1.9249	-0.7871	-1.6795	0.6135	0.3429	0.0572	0.0102	0.588	-0.0971	0.4938	-3.6783	10.9236	25.1088
14	1.0899	-0.9049	-0.4	0.872	1.1171	4.2474	0.187	-0.5665	0.0884	1.2194	-0.1424	0.1702	0.3476	0.1961	0.0322	1.0313	-0.4278	0.3956	0.5922	-0.3577	0.1484	-1.754	6.3235	38.6692
15	1.6312	0.4539	1.4952	1.8091	1.7369	2.6936	-0.2417	-0.1581	-0.6342	0.7705	-0.2992	-0.5977	1.7706	-0.4062	0.5001	0.8348	-0.2657	0.1638	0.4155	-0.0599	0.5388	-3.4962	-1.7968	36.5734
16	6.3752	2.8159	-7.2411	4.0703	-3.8932	8.4014	-0.4943	0.3016	-0.1268	-0.2709	0.4565	-0.5268	-0.5658	-0.8143	0.0435	0.6548	-0.1989	-0.1566	0.7713	-0.069	0.6196	-10.1204	1.47	39.7912
17	0.5243	0.3082	0.22	4.5557	0.2987	3.9904	0.1077	-0.4199	-0.8699	0.5596	-0.147	0.9642	-0.8655	-0.3816	0.0309	0.4616	-0.0509	0.221	1.2673	-0.1833	0.6294	-12.197	7.9456	33.8162
18	1.9998	0.1766	6.7422	1.4423	0.699	4.4624	0.7358	-2.5507	0.896	1.3315	-1.4237	0.4218	0.3665	-1.4694	0.6968	0.6928	-0.3142	0.0522	1.1835	-0.1719	0.5609	-9.2136	5.0799	52.3694
19	3.754	-2.9414	-4.1485	2.3422	3.2674	4.5278	0.2259	-0.7245	0.4425	1.0022	-0.4888	0.2604	-0.0953	-0.0193	0.0967	0.5053	-0.1879	0.165	0.4487	-0.1963	0.312	0.8215	10.6651	34.5519
20	5.2135	-6.0749	-4.9645	7.0777	5.7734	4.665	-0.0227	-0.4262	0.3016	0.5744	-0.0692	-0.1831	-0.0067	0.0254	0.0329	0.2506	-0.0606	0.0465	0.2603	-0.0342	0.2811	7.5622	9.4209	28.3101
21	1.1587	0.7082	0.8756	1.2121	0.8282	0.7736	-0.4393	0.4136	-0.3909	-0.1262	0.1906	-0.0061	1.0148	-1.2745	0.4046	1.0381	-0.5244	0.246	0.8191	-0.5385	0.3672	-6.6188	15.4102	46.3135

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 225 through 327 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 328 through 390 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 391 through 455 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 456 through 491 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 492 through 508 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 509 through 538 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 225 through 327 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 328 through 390 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 391 through 538 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 1 through 5 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 6 through 12 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 19 through 23 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 24 through 32 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 33 through 52 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 53 through 63 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 64 through 72 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 73 through 82 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 83 through 89 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 92 through 101 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 102 through 109 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 110 through 117 )

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