PDB-7yqg: Functional and Structural Characterization of Norovirus GII.6 in ...

ID or keywords:

Entry

Database: PDB / ID: 7yqg

Title

Functional and Structural Characterization of Norovirus GII.6 in Recognizing Histo-blood Group Antigens

Components

VP1

Keywords

VIRAL PROTEIN /

Complex

Function / homology

Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein /

Viral coat protein subunit / VP1

Function and homology information

Biological species

Norovirus GII

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.698 Å

Authors

Duan, Z.J. / Cong, X.

Funding support

China, 1items

Citation

Journal: Virol Sin / Year: 2023
Title: Functional and structural characterization of Norovirus GII.6 in recognizing histo-blood group antigens.
Authors: Cong, X. / Li, H.B. / Sun, X.M. / Qi, J.X. / Zhang, Q. / Duan, Z.J. / Xu, Y. / Liu, W.L.

History

Deposition	Aug 6, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 7, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7yqg.cif.gz	282 KB	Display	PDBx/mmCIF format
PDB format	pdb7yqg.ent.gz	227.3 KB	Display	PDB format
PDBx/mmJSON format	7yqg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yq/7yqg ftp://data.pdbj.org/pub/pdb/validation_reports/yq/7yqg	HTTPS FTP

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Related structure data

Related structure data	7yqbC 4rlzS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (4)

Deposited unit

A: VP1

B: VP1

hetero molecules

70.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	62.631, 94.597, 108.968
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein

VP1 / norovirus P domain protein

Mass: 34835.855 Da / Num. of mol.: 2 / Mutation: Q304P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Norovirus GII / Gene: ORF2 / Production host:

Escherichia coli (E. coli) / References: UniProt: A0A2U9GLY1

#2: Polysaccharide

alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose

Type: oligosaccharide

/ Mass: 326.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

#3: Chemical

ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL /

Glycerol

Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃

#4: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 771 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

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: 2.32 Å³/Da / Density % sol: 46.97 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.2 M calcium chloride dihydrate, 0.1 M sodium acetate trihydrate pH 4.6, 20% (vol/vol) 2-propanol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 12, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.698→50 Å / Num. obs: 72108 / % possible obs: 99.28 % / Redundancy: 10.4 % / R_merge(I) obs: 0.072 / Net I/σ(I): 39.868
Reflection shell	Resolution: 1.7→1.76 Å / R_merge(I) obs: 0.072 / Num. unique obs: 71619

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Processing

Software

Name	Version	Classification
PHENIX	(1.15.2_3472: ???)	refinement
PDB_EXTRACT	3.27	data extraction
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4RLZ

4rlz

Resolution: 1.698→47.299 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.82 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1746	3710	5.18 %
R_work	0.1427	-	-
obs	0.1443	71619	99.25 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.698→47.299 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4730	0	0	771	5501

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4888
X-RAY DIFFRACTION	f_angle_d	0.77	6692
X-RAY DIFFRACTION	f_dihedral_angle_d	7.185	3840
X-RAY DIFFRACTION	f_chiral_restr	0.054	743
X-RAY DIFFRACTION	f_plane_restr	0.006	884

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 (%)
1.698-1.7201	0.2264	119	0.1946	2341	X-RAY DIFFRACTION	90
1.7201-1.7437	0.2158	129	0.1874	2485	X-RAY DIFFRACTION	95
1.7437-1.7686	0.2012	154	0.1702	2537	X-RAY DIFFRACTION	99
1.7686-1.795	0.2224	143	0.1631	2550	X-RAY DIFFRACTION	99
1.795-1.823	0.2033	130	0.1568	2617	X-RAY DIFFRACTION	99
1.823-1.8529	0.2091	161	0.1563	2573	X-RAY DIFFRACTION	99
1.8529-1.8849	0.2052	155	0.1589	2556	X-RAY DIFFRACTION	100
1.8849-1.9192	0.1902	133	0.1554	2609	X-RAY DIFFRACTION	100
1.9192-1.9561	0.1972	148	0.1506	2628	X-RAY DIFFRACTION	100
1.9561-1.996	0.1585	156	0.1457	2567	X-RAY DIFFRACTION	100
1.996-2.0394	0.1848	131	0.1403	2623	X-RAY DIFFRACTION	100
2.0394-2.0869	0.2332	139	0.1362	2619	X-RAY DIFFRACTION	100
2.0869-2.139	0.1866	141	0.1406	2613	X-RAY DIFFRACTION	100
2.139-2.1969	0.1659	144	0.1369	2601	X-RAY DIFFRACTION	100
2.1969-2.2615	0.1579	124	0.1344	2638	X-RAY DIFFRACTION	100
2.2615-2.3345	0.1676	167	0.1399	2602	X-RAY DIFFRACTION	100
2.3345-2.4179	0.1729	169	0.1383	2632	X-RAY DIFFRACTION	100
2.4179-2.5148	0.1898	151	0.1438	2591	X-RAY DIFFRACTION	100
2.5148-2.6292	0.1729	132	0.1427	2653	X-RAY DIFFRACTION	100
2.6292-2.7678	0.172	132	0.1476	2656	X-RAY DIFFRACTION	100
2.7678-2.9412	0.1824	147	0.1464	2615	X-RAY DIFFRACTION	100
2.9412-3.1682	0.1832	128	0.1392	2679	X-RAY DIFFRACTION	100
3.1682-3.487	0.1657	137	0.1332	2689	X-RAY DIFFRACTION	100
3.487-3.9913	0.1709	129	0.1256	2685	X-RAY DIFFRACTION	100
3.9913-5.0277	0.1263	159	0.1189	2705	X-RAY DIFFRACTION	100
5.0277-47.299	0.159	152	0.159	2845	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	1.2868	-0.3366	0.138	0.6854	0.3731	0.7659	-0.2143	0.1039	-0.0094	0.0534	0.115	0.0922	-0.2518	-0.1996	-0.0211	0.1387	0.0349	-0.0298	0.0801	0.0114	0.0845	68.0144	106.5258	22.1011
2	1.5318	-0.4021	-1.1252	1.0004	0.8188	2.5606	-0.1341	-0.1058	-0.1573	0.2089	0.0514	0.0346	0.2636	-0.0567	0.0172	0.1127	0.0202	-0.0023	0.0838	-0.0119	0.1197	73.1632	96.1313	28.05
3	3.0743	0.6686	2.9961	0.3085	1.204	4.7863	0.203	-0.2735	-0.4661	0.2544	0.0864	-0.1137	0.7503	-0.2037	-0.1651	0.4486	0.0175	-0.1732	0.2758	0.0312	0.2299	76.3747	99.113	44.4887
4	0.9795	-0.147	0.1618	1.0457	-0.0629	1.4623	-0.0269	-0.0279	0.0525	0.0234	0.0685	0.0085	-0.2139	0.0398	0.0036	0.0998	-0.0071	-0.0054	0.0638	-0.0132	0.0997	81.2504	108.7584	23.8464
5	3.0118	-0.0564	-1.2327	0.9977	0.0768	1.9302	-0.104	0.0856	-0.1836	-0.1373	0.1235	-0.2595	0.0214	0.3611	-0.0329	0.0656	0.0099	0.0364	0.2009	-0.0402	0.168	94.6028	96.5078	12.7412
6	0.5282	0.1131	0.187	0.5436	0.4072	1.6406	-0.004	0.1097	0.0226	-0.0048	0.1206	-0.2115	0.0412	0.3575	-0.0224	0.0695	0.0048	0.0045	0.1792	-0.0231	0.1474	95.3039	95.48	14.255
7	0.8029	-0.1194	-0.0323	1.1157	0.4164	1.2466	-0.04	-0.0604	0.1317	0.1198	0.1251	-0.2005	0.0236	0.2672	-0.0005	0.0697	0.0002	-0.0223	0.1188	-0.0201	0.1146	90.1568	100.5549	28.0441
8	0.5232	-0.2077	0.0683	1.0424	0.2821	1.3762	0.0073	-0.082	0.0119	0.0924	-0.0249	0.0593	-0.1157	-0.1461	-0.0256	0.0753	0.0204	-0.001	0.0723	-0.0128	0.0794	71.2776	105.0595	28.5339
9	1.6249	-0.142	0.0719	1.2427	0.5109	2.0999	-0.0292	-0.0934	-0.1667	0.1564	0.0208	0.0764	-0.0574	-0.2858	0.0145	0.1379	0.0455	0.0087	0.1394	-0.0004	0.124	64.8329	109.1506	35.4437
10	0.4428	-0.0373	0.6293	1.6618	0.1556	1.1474	-0.0192	-0.0228	0.1138	0.0263	-0.0387	-0.065	-0.1996	-0.0406	0.0031	0.1008	0.009	0.0111	0.0706	-0.0122	0.1	70.673	108.6155	6.9587
11	0.4923	-0.0966	0.5072	1.2126	-1.3283	1.8216	-0.0234	0.1308	0.0196	-0.1067	-0.1092	-0.3373	0.0689	0.2369	0.0389	0.1019	0.0176	0.0094	0.0987	-0.001	0.1224	78.6056	100.2614	0.8597
12	0.6093	0.8061	1.1606	1.0602	1.5463	2.3383	0.105	0.059	-0.2744	-0.183	0.1297	-0.2472	0.152	0.4702	-0.0813	0.2475	0.0212	0.0155	0.326	-0.0735	0.2286	74.5793	98.0788	-15.4467
13	0.709	0.0408	0.2004	1.0331	-0.1154	1.5215	0.0303	-0.0382	0.0874	-0.0393	0.0165	0.0209	0.0631	-0.2264	-0.0185	0.0677	-0.0117	-0.0036	0.0808	0.0073	0.0856	64.2071	96.7568	5.5954
14	0.963	0.0427	-0.2038	2.0203	-0.7547	0.9696	0.0275	-0.0058	-0.2849	-0.027	0.0085	-0.1272	0.2299	0.0377	-0.0392	0.1605	-0.0164	-0.0179	0.052	0.0207	0.1224	70.6585	78.2334	15.9686
15	0.7777	0.1643	0.2879	0.6218	-0.1781	1.4043	0.0634	-0.0425	-0.1486	-0.0064	0.0216	0.0404	0.2389	-0.0482	-0.0535	0.144	-0.0203	-0.0123	0.0563	0.0099	0.1028	71.9256	78.9582	14.4454
16	0.9977	-0.1254	0.2328	0.9042	-0.3723	1.2895	0.044	0.0863	-0.1133	-0.1185	0.018	0.1294	0.2157	-0.0737	-0.0212	0.1092	-0.0289	-0.0121	0.0629	0.0001	0.0839	68.5723	85.7579	0.916
17	0.6225	-0.3375	0.1002	0.6875	0.073	0.946	-0.0129	0.0688	0.0952	-0.089	0.0113	-0.0158	-0.0623	-0.0671	-0.0025	0.0754	0.0042	0.004	0.0793	0.0078	0.0924	69.9193	106.3659	-0.8655
18	1.4603	-0.3329	1.1397	0.0906	-0.2709	0.8689	-0.0084	0.4056	-0.2769	-0.2179	0.3584	-0.4041	-0.1501	0.8063	-0.1882	0.1754	-0.048	0.0192	0.2709	-0.0196	0.2657	80.1219	110.767	-7.3784
19	0.8084	-0.3045	0.248	0.9639	-0.2538	2.7895	0.0482	0.1607	0.1698	-0.2474	-0.1168	0.0481	-0.1685	-0.1723	0.023	0.1425	0.0264	-0.0034	0.1562	0.0347	0.1619	64.6245	115.0053	-6.4507

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 20 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 21 through 30 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 31 through 35 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 36 through 61 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 62 through 72 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 88 through 174 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 175 through 212 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 213 through 270 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 271 through 317 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 4 through 20 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 21 through 30 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 31 through 35 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 36 through 61 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 62 through 73 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 87 through 174 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 175 through 212 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 213 through 287 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 288 through 300 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 301 through 317 )

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