PDB-6h6z: GI.1 human norovirus protruding domain in complex with Nano-62

ID or keywords:

Entry

Database: PDB / ID: 6h6z

Title

GI.1 human norovirus protruding domain in complex with Nano-62

Components

Capsid protein VP1
Nanobody (VHH) Nano-62

Keywords

VIRAL PROTEIN / Norovirus / GI.1 / P domain / Nano-62

Function / homology

Function and homology information

T=3 icosahedral viral capsid / host cell cytoplasm / identical protein binding
Similarity search - Function

Biological species

Norwalk virus

Vicugna pacos (alpaca)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.085 Å

Authors

Kilic, T. / Hansman, G.S.

Citation

Journal: J. Virol. / Year: 2019
Title: Structural Basis of Nanobodies Targeting the Prototype Norovirus.
Authors: Ruoff, K. / Kilic, T. / Devant, J. / Koromyslova, A. / Ringel, A. / Hempelmann, A. / Geiss, C. / Graf, J. / Haas, M. / Roggenbach, I. / Hansman, G.

History

Deposition	Jul 30, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 19, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 23, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Mar 13, 2019	Group: Data collection / Database references Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.3	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6h6z.cif.gz	322.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6h6z.ent.gz	260.4 KB	Display	PDB format
PDBx/mmJSON format	6h6z.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6h6z_validation.pdf.gz	460 KB	Display	wwPDB validaton report
Full document	6h6z_full_validation.pdf.gz	464.5 KB	Display
Data in XML	6h6z_validation.xml.gz	31.2 KB	Display
Data in CIF	6h6z_validation.cif.gz	44.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h6/6h6z ftp://data.pdbj.org/pub/pdb/validation_reports/h6/6h6z	HTTPS FTP

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Related structure data

Related structure data	6h6yC 6h70C 6h71C 6h72C 2zl5S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6h70-d 3iyx-d 1o9l-1 2yi9-4 5ejm-1 4zgv-1 2yi8-1 2jla-1 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	#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) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (1)

Deposited unit

A: Capsid protein VP1

B: Capsid protein VP1

C: Nanobody (VHH) Nano-62

D: Nanobody (VHH) Nano-62

hetero molecules

94.1 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)	172.240, 89.640, 61.920
Angle α, β, γ (deg.)	90.00, 107.80, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Capsid protein VP1 / CP / p59 Mass: 31182.939 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Norwalk virus (strain GI/Human/United States/Norwalk/1968) Strain: GI/Human/United States/Norwalk/1968 / Gene: ORF2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q83884
#2: Antibody	Nanobody (VHH) Nano-62 Mass: 15651.546 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Alpaca / Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.43 Å³/Da / Density % sol: 49.37 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium citrate (pH 5.5) and 20% (w/v) PEG3000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9677 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 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: 2.09→46.67 Å / Num. obs: 51659 / % possible obs: 96.9 % / Redundancy: 4 % / R_merge(I) obs: 0.071 / Net I/σ(I): 11.2
Reflection shell	Resolution: 2.09→2.16 Å / R_merge(I) obs: 0.554 / Mean I/σ(I) obs: 1.7 / % possible all: 82.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2ZL5

2zl5

Resolution: 2.085→46.672 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.62 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2167	2576	5 %
R_work	0.1781	-	-
obs	0.1801	51566	96.36 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.085→46.672 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6079	0	30	219	6328

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6279
X-RAY DIFFRACTION	f_angle_d	0.893	8596
X-RAY DIFFRACTION	f_dihedral_angle_d	7.52	3639
X-RAY DIFFRACTION	f_chiral_restr	0.059	962
X-RAY DIFFRACTION	f_plane_restr	0.006	1125

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 (%)
2.0851-2.1252	0.4123	94	0.3909	1811	X-RAY DIFFRACTION	63
2.1252-2.1686	0.3161	145	0.289	2730	X-RAY DIFFRACTION	99
2.1686-2.2157	0.3108	147	0.2459	2813	X-RAY DIFFRACTION	99
2.2157-2.2673	0.2974	145	0.2429	2750	X-RAY DIFFRACTION	98
2.2673-2.324	0.2878	146	0.2272	2751	X-RAY DIFFRACTION	98
2.324-2.3868	0.2621	145	0.2192	2789	X-RAY DIFFRACTION	99
2.3868-2.457	0.2741	143	0.2172	2756	X-RAY DIFFRACTION	98
2.457-2.5363	0.2531	146	0.2097	2752	X-RAY DIFFRACTION	98
2.5363-2.627	0.2718	146	0.2028	2773	X-RAY DIFFRACTION	98
2.627-2.7321	0.2843	145	0.1935	2750	X-RAY DIFFRACTION	97
2.7321-2.8565	0.2584	144	0.1972	2746	X-RAY DIFFRACTION	97
2.8565-3.007	0.2432	140	0.1934	2648	X-RAY DIFFRACTION	95
3.007-3.1954	0.235	142	0.1859	2698	X-RAY DIFFRACTION	95
3.1954-3.442	0.1938	149	0.176	2828	X-RAY DIFFRACTION	100
3.442-3.7883	0.1947	148	0.1698	2811	X-RAY DIFFRACTION	100
3.7883-4.3361	0.1809	149	0.1424	2839	X-RAY DIFFRACTION	100
4.3361-5.4617	0.1667	150	0.1344	2851	X-RAY DIFFRACTION	100
5.4617-46.6833	0.191	152	0.1661	2894	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	1.3496	-0.1877	-0.2128	1.1196	-0.2012	0.6045	-0.0188	0.0371	-0.027	0.0385	0.0561	0.0616	0.0118	-0.0553	-0.0275	0.2932	-0.0038	0.0105	0.3327	-0.0317	0.2964	191.7714	0.7402	32.6539
2	4.3506	0.2909	-1.7251	2.3005	-2.3904	3.1017	-0.1006	-0.1214	-0.043	0.43	0.1162	-0.2695	-0.2183	0.1798	-0.0141	0.3364	0.0317	-0.0282	0.3103	-0.1085	0.3229	203.844	-2.2205	36.2204
3	2.23	-0.2667	-0.6645	7.6942	-3.2377	8.0591	-0.1778	-0.1229	-0.3952	0.1575	0.1363	-0.1394	0.3281	-0.0517	0.0998	0.167	0.0532	0.0039	0.3616	-0.023	0.364	206.2929	-9.9516	37.5015
4	1.5642	-0.1069	0.0745	2.5534	0.5281	0.9877	-0.1044	0.4272	0.1597	-0.2701	0.0902	0.0308	-0.0405	0.0821	0.0048	0.2798	-0.0686	0.0138	0.4703	0.0534	0.2698	196.1919	15.0472	10.0841
5	0.8634	-0.0951	-0.1411	0.959	-0.0297	1.0811	-0.0347	0.5923	0.064	-0.4492	0.101	0.0388	-0.0485	-0.0293	0.0082	0.3798	-0.107	-0.0103	0.5857	0.0184	0.2911	195.2369	9.4014	0.2356
6	2.4606	-0.1592	-0.5874	1.6007	0.3151	2.6395	-0.159	0.7538	-0.1325	-0.3914	0.2066	0.119	0.2399	-0.0374	-0.0292	0.4585	-0.0892	0.0186	0.5905	-0.1413	0.3156	197.69	-10.5362	-1.4077
7	6.0333	-0.5774	0.0549	1.5764	-0.7478	1.5418	-0.2159	0.8562	0.2085	-0.3592	0.181	-0.3543	-0.0524	0.4677	-0.0066	0.3906	-0.1312	0.0738	0.7457	-0.0931	0.5736	227.8582	8.7701	10.3108
8	5.1085	-5.0248	1.2907	4.9587	-1.4707	4.9417	0.2088	0.2168	0.3336	0.5963	-0.5456	-0.0014	0.1009	-0.1701	0.2593	0.422	-0.0125	0.0488	0.6161	-0.1377	0.6983	228.009	4.9541	20.9176
9	5.0497	1.7915	-0.6188	1.2771	-0.4976	1.5554	-0.2925	0.9208	0.1894	-0.1095	0.3898	-0.5816	-0.0752	0.4726	-0.0727	0.3443	-0.0699	0.0495	0.6974	-0.094	0.6267	229.2326	7.0897	12.4218
10	2.9363	3.0688	-1.2555	3.1822	-1.3238	0.8742	-0.0159	-0.1259	-0.0161	0.6231	-0.0352	1.0874	0.3492	-0.0178	0.0341	0.3809	-0.0535	0.0328	0.5015	-0.0081	0.6815	169.4117	-31.2089	26.0077
11	1.9847	0.3996	-0.6427	2.4004	-2.0184	1.7536	-0.0675	-0.0828	-0.0504	-0.0714	0.1605	0.6029	0.1633	0.084	-0.0971	0.3241	-0.0531	0.0101	0.4121	-0.0899	0.534	175.9253	-22.5015	21.8001
12	1.2938	0.6548	0.2778	6.678	-6.1272	9.1715	-0.3046	-0.1826	-0.0512	-0.4983	0.3212	-0.042	0.3234	-0.2661	0.2662	0.3988	-0.0273	-0.0152	0.478	-0.0616	0.5566	180.4256	-28.3341	17.1926
13	1.5771	2.0089	-0.7038	4.8087	-0.2393	2.8135	-0.045	0.156	-0.2996	-0.383	0.0052	0.2142	0.2578	-0.2264	0.0787	0.4115	-0.0375	0.0104	0.4515	-0.0531	0.6459	173.3564	-31.1754	18.8486
14	2.4284	1.0621	-1.3062	3.2254	-0.914	2.5465	0.028	-0.1396	-0.216	0.2476	0.1183	0.1691	0.044	0.2182	-0.0805	0.342	0.0006	0.0177	0.4385	-0.0606	0.5599	182.2618	-26.3423	22.7396
15	2.6687	0.3786	0.0876	3.4905	-1.6028	0.7761	-0.0388	0.2494	0.0556	-0.3405	0.0892	-0.3816	0.0563	0.2062	-0.0041	0.2889	0.002	0.0061	0.3166	-0.0493	0.2107	199.6782	-0.6883	23.6392
16	3.8496	-0.9751	-0.0137	1.5457	-0.7044	1.2655	-0.0035	0.0992	-0.2777	0.0144	0.0578	0.3628	0.0584	-0.1172	-0.0857	0.2521	-0.0446	0.0397	0.3281	-0.016	0.3227	181.4131	0.1182	25.4071
17	1.5838	0.0414	-0.009	1.1586	-0.5889	1.1937	-0.073	0.2055	0.0619	0.0396	0.1391	0.284	0.024	-0.3589	-0.084	0.2559	-0.0006	0.0329	0.413	0.0418	0.4109	175.3059	12.4946	23.2033

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 378 through 468 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 469 through 499 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 500 through 518 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 228 through 377 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 378 through 448 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 449 through 518 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 1 through 52 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 53 through 64 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 65 through 126 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 1 through 17 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 18 through 39 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 40 through 60 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 61 through 99 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 100 through 126 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 228 through 251 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 252 through 321 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 322 through 377 )

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