PDB-6h71: GI.1 human norovirus protruding domain in complex with Nano-94

ID or keywords:

Entry

Database: PDB / ID: 6h71

Title

GI.1 human norovirus protruding domain in complex with Nano-94

Components

Capsid protein VP1
Nanobody (VHH) Nano-94

Keywords

VIRAL PROTEIN / Norovirus / GI.1 / P domain / Nano-94

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: 2.313 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 / 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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Download

PDBx/mmCIF format	6h71.cif.gz	317 KB	Display	PDBx/mmCIF format
PDB format	pdb6h71.ent.gz	259.3 KB	Display	PDB format
PDBx/mmJSON format	6h71.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6h71_validation.pdf.gz	454.4 KB	Display	wwPDB validaton report
Full document	6h71_full_validation.pdf.gz	457.2 KB	Display
Data in XML	6h71_validation.xml.gz	29.2 KB	Display
Data in CIF	6h71_validation.cif.gz	40.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h7/6h71 ftp://data.pdbj.org/pub/pdb/validation_reports/h7/6h71	HTTPS FTP

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Related structure data

Related structure data	6h6yC 6h6zC 6h70C 6h72C 2zl5S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6h72-d 4wc3-d 0502 4x7d-d 4wc2-d 4x7c-d 4wc7-d 4wc5-d 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-94

D: Nanobody (VHH) Nano-94

hetero molecules

92.5 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)	94.890, 111.060, 122.460
Angle α, β, γ (deg.)	90.00, 99.81, 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-94 Mass: 14928.474 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.22 Å³/Da / Density % sol: 44.58 %
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: ID29 / Wavelength: 0.97895 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97895 Å / Relative weight: 1
Reflection	Resolution: 2.31→49.4 Å / Num. obs: 53187 / % possible obs: 97.19 % / Redundancy: 2.9 % / B_iso Wilson estimate: 48.98 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.05036 / R_pim(I) all: 0.03398 / R_rim(I) all: 0.061 / Net I/σ(I): 14.21
Reflection shell	Resolution: 2.31→2.4 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.5433 / Mean I/σ(I) obs: 2.08 / Num. unique obs: 5051 / CC_1/2: 0.874 / R_pim(I) all: 0.3624 / R_rim(I) all: 0.6556 / % possible all: 92.74

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS	VERSION Nov 1, 2016	data reduction
XSCALE	VERSION Nov 1, 2016	data scaling
PHASER	VERSION Nov 1, 2016	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2ZL5

2zl5

Resolution: 2.313→49.4 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.14

	R_factor	Num. reflection	% reflection
R_free	0.217	2658	5 %
R_work	0.1925	-	-
obs	0.1937	53108	97.2 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.313→49.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5967	0	16	129	6112

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	6171
X-RAY DIFFRACTION	f_angle_d	0.62	8465
X-RAY DIFFRACTION	f_dihedral_angle_d	4.899	4018
X-RAY DIFFRACTION	f_chiral_restr	0.047	950
X-RAY DIFFRACTION	f_plane_restr	0.005	1109

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 (%)
2.3134-2.3554	0.3495	127	0.3153	2421	X-RAY DIFFRACTION	88
2.3554-2.4007	0.3137	139	0.277	2630	X-RAY DIFFRACTION	98
2.4007-2.4497	0.3085	141	0.2775	2676	X-RAY DIFFRACTION	98
2.4497-2.503	0.3085	142	0.2567	2690	X-RAY DIFFRACTION	98
2.503-2.5612	0.2814	139	0.2568	2623	X-RAY DIFFRACTION	98
2.5612-2.6253	0.2371	142	0.2503	2689	X-RAY DIFFRACTION	98
2.6253-2.6963	0.3173	140	0.2565	2665	X-RAY DIFFRACTION	98
2.6963-2.7756	0.2803	142	0.2481	2688	X-RAY DIFFRACTION	98
2.7756-2.8652	0.2745	139	0.2291	2667	X-RAY DIFFRACTION	98
2.8652-2.9676	0.2824	141	0.2193	2666	X-RAY DIFFRACTION	99
2.9676-3.0864	0.2225	142	0.2177	2693	X-RAY DIFFRACTION	98
3.0864-3.2268	0.2238	140	0.2091	2670	X-RAY DIFFRACTION	98
3.2268-3.3969	0.2468	141	0.2042	2681	X-RAY DIFFRACTION	98
3.3969-3.6097	0.2254	140	0.1981	2648	X-RAY DIFFRACTION	98
3.6097-3.8883	0.214	139	0.1883	2650	X-RAY DIFFRACTION	97
3.8883-4.2793	0.1992	142	0.1596	2690	X-RAY DIFFRACTION	97
4.2793-4.8981	0.1623	141	0.141	2671	X-RAY DIFFRACTION	97
4.8981-6.1692	0.1594	139	0.1635	2659	X-RAY DIFFRACTION	96
6.1692-49.4131	0.1914	142	0.1711	2673	X-RAY DIFFRACTION	96

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	3.8927	3.4184	-0.838	10.0387	-3.6529	2.0306	-0.0891	-0.1	0.9838	0.1905	0.2133	1.5037	-0.327	-0.2964	-0.0712	0.5396	0.091	-0.0518	0.4497	0.0584	0.6972	155.2373	37.1873	128.1645
2	2.0579	1.7426	-0.4428	7.1967	-3.7873	1.9239	-0.0295	-0.1195	0.1405	-0.0594	-0.0868	-0.0517	0.0357	-0.0568	0.1241	0.4033	0.0022	-0.0209	0.4185	0.0298	0.3255	159.5045	25.1394	127.0588
3	0.4265	-0.1231	-0.6162	2.9422	2.9227	3.23	0.111	0.1449	-0.144	0.7691	0.1196	-0.0983	1.1174	1.1	-0.2771	1.1019	0.0961	-0.2494	0.8144	0.0176	0.5008	177.9792	-2.9284	193.1573
4	4.5847	-1.8952	-2.2082	4.7778	1.2846	5.8713	0.7006	0.5861	-0.0209	0.002	-0.3423	-0.1013	0.0574	0.6616	-0.4019	0.6809	-0.0784	-0.0608	0.7273	-0.0337	0.452	180.6373	8.2422	188.6679
5	0.8282	1.1517	1.3274	3.1078	5.1068	8.3698	0.4145	0.0063	-0.1561	0.3885	0.1216	-0.407	0.8267	0.8581	-0.5132	0.8702	0.0407	-0.1554	0.6965	-0.022	0.4611	178.5685	0.1286	188.6329
6	8.5689	-3.4545	-1.1976	2.3119	0.4279	9.5947	0.6555	-0.0689	0.6208	0.3666	0.4463	-0.1608	0.2496	0.2591	-1.1143	0.8528	-0.1747	0.0856	0.4544	-0.0438	0.4214	172.8187	10.3056	202.6905
7	2.9921	3.583	1.414	6.157	-1.8881	7.6878	0.2297	-0.1769	-0.2137	0.3529	0.0369	-0.0986	0.3711	0.2846	-0.3423	0.2597	0.0509	-0.0143	0.3408	0.0245	0.2733	156.1503	-12.0519	144.0588
8	2.612	0.5742	0.0741	3.5966	-0.7415	3.5901	-0.1384	0.1577	0.1698	0.0605	0.298	0.5702	-0.2662	-0.6218	-0.1832	0.4244	0.0212	-0.014	0.49	0.047	0.3993	149.5903	-0.1319	134.8223
9	1.421	0.2036	0.6209	2.963	-0.5539	2.237	0.0019	0.0141	0.0708	-0.0307	-0.0016	-0.1323	-0.1658	0.0489	0.0005	0.3204	0.0129	0.011	0.3365	0.0028	0.2678	163.0491	5.004	138.7497
10	5.1979	-0.129	2.1507	3.008	0.9575	5.5066	0.2065	-0.0037	-0.3515	0.0129	0.0682	0.1437	0.6951	-0.5607	-0.3028	0.514	-0.1233	-0.0782	0.366	0.0317	0.4144	147.8995	-17.3656	135.9375
11	4.5917	0.6442	2.5999	2.6051	0.8973	6.9052	0.2965	-0.4103	-0.1684	-0.1527	0.0167	0.2555	0.1549	-0.7004	-0.2269	0.4429	-0.17	-0.0355	0.4234	0.1204	0.4713	143.1771	-15.7833	136.2429
12	2.2458	-0.6262	0.246	2.0311	0.2431	4.1486	0.0033	-0.3677	-0.0896	0.3298	0.1225	-0.0983	0.2379	-0.054	-0.1733	0.4359	0.0073	-0.0716	0.3749	0.0342	0.2833	168.6452	-11.6031	156.488
13	2.7734	-2.2682	0.8196	4.2177	2.7654	5.1843	-0.1321	-0.407	-0.5379	0.8362	0.2303	0.5057	0.999	-1.0764	-0.0388	0.6895	-0.0348	0.0125	0.7087	0.098	0.4044	156.9265	-8.4673	165.381
14	2.1377	-0.1973	0.3613	2.9165	-0.6546	4.7878	-0.2275	-0.426	0.0963	0.5824	0.1536	-0.2091	-0.5652	-0.1783	0.0861	0.6813	0.0567	-0.0982	0.5285	-0.0793	0.3337	166.6975	3.6259	165.6746
15	5.8798	-3.0636	3.0947	8.4759	4.6125	7.3371	-0.3826	-1.0355	-0.383	1.384	0.0032	0.2727	0.7029	0.2396	0.4393	0.7129	0.0839	-0.1006	0.5507	0.0464	0.4458	172.0881	-10.6983	171.2528
16	1.5424	-0.0544	0.3803	4.1894	-0.4261	3.2393	0.0533	-0.1575	-0.1712	0.5779	-0.0847	-0.357	0.4178	0.5421	0.0476	0.5298	0.0669	-0.1181	0.5622	0.006	0.3834	178.4655	-13.8562	158.1823
17	5.0603	-1.4739	-0.4913	2.1183	1.3058	1.9973	-0.0151	-0.0313	-0.5329	0.1695	0.0054	-0.008	0.3946	0.3115	0.0078	0.5471	0.0473	-0.062	0.4426	0.0226	0.3409	169.6354	-24.2132	147.6613
18	3.8808	-0.041	0.6447	5.3501	-3.4126	4.4114	-0.0622	0.0776	-0.4373	0.0843	-0.4326	-0.7188	0.4747	0.4502	0.4384	0.5661	0.1689	-0.0541	0.5805	0.0252	0.5143	179.5048	-24.5415	147.9768
19	4.5887	-2.49	0.8608	5.2929	-2.4385	3.3338	0.212	-0.0143	-0.1006	-0.0601	-0.1916	-0.7097	0.414	0.6323	0.0038	0.6068	0.1659	-0.0483	0.6269	-0.0715	0.5271	182.6418	-25.6353	148.1428
20	2.6917	3.0163	-0.7407	8.8397	-2.2418	0.8228	-0.0724	-0.0131	0.215	-0.8451	0.2807	0.7239	0.2724	-0.0902	-0.2155	0.5334	0.0511	-0.105	0.3998	0.0645	0.4962	158.2115	32.1392	124.541
21	6.0591	3.0689	-0.5077	8.1271	0.4023	8.4176	0.6831	-1.35	-0.2087	1.3069	-0.6976	1.7286	0.1907	-0.8906	0.0608	0.6535	0.0981	0.1738	0.4924	0.0391	0.8605	150.8724	32.5331	133.3787

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 60 through 99 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 100 through 121 )
3	X-RAY DIFFRACTION	3	chain 'D' and (resid 1 through 33 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 34 through 66 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 67 through 114 )
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 115 through 121 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 229 through 251 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 252 through 269 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 270 through 448 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 449 through 484 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 485 through 516 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 230 through 301 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 302 through 321 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 322 through 387 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 388 through 403 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 404 through 438 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 439 through 463 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 464 through 483 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 484 through 516 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 1 through 45 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 46 through 59 )

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