PDB-4qvj: Unliganded crystal structure of Feline Norovirus P Domain co-crys...

ID or keywords:

Entry

Database: PDB / ID: 4qvj

Title

Unliganded crystal structure of Feline Norovirus P Domain co-crystallized with N-acetylneuraminic acid

Components

VP1

Keywords

VIRAL PROTEIN / Feline Norovirus / Viral Capsid Protein / P domain / Protruding Domain

Function / homology

Function and homology information

Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...
Similarity search - Domain/homology

Biological species

Norovirus cat/GIV.2/CU081210E/USA/2010

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.26 Å

Authors

Singh, B.K. / Hansman, G.S.

Citation

Journal: Virology / Year: 2015
Title: Structural analysis of a feline norovirus protruding domain.
Authors: Singh, B.K. / Glatt, S. / Ferrer, J.L. / Koromyslova, A.D. / Leuthold, M.M. / Dunder, J. / Hansman, G.S.

History

Deposition	Jul 15, 2014	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Nov 19, 2014	Provider: repository / Type: Initial release
Revision 1.1	Mar 4, 2015	Group: Database references
Revision 1.2	Mar 20, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	4qvj_validation.pdf.gz	432.1 KB	Display	wwPDB validaton report
Full document	4qvj_full_validation.pdf.gz	435.1 KB	Display
Data in XML	4qvj_validation.xml.gz	27 KB	Display
Data in CIF	4qvj_validation.cif.gz	38.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qv/4qvj ftp://data.pdbj.org/pub/pdb/validation_reports/qv/4qvj	HTTPS FTP

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Related structure data

Related structure data	4quzC 4qv2C 4qvaC C: citing same article (ref.)
Similar structure data	4jx1-2 1zj8-1 4qv2-d 2m56-d 4quz-d 4jwu-1 4qva-d 4k4v-1 4jws-2 2e8q-d Search similar-shape structures by Omokage search (details) 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

73.3 kDa, 2 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)	57.700, 99.600, 129.920
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	VP1 Mass: 36662.984 Da / Num. of mol.: 2 / Fragment: P domain (UNP RESIDUES 225-565) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Norovirus cat/GIV.2/CU081210E/USA/2010 / Gene: JF781268 / Plasmid: MBP-HTSHP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H8YRY9
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

VP1

Mass: 36662.984 Da / Num. of mol.: 2 / Fragment: P domain (UNP RESIDUES 225-565)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Norovirus cat/GIV.2/CU081210E/USA/2010 / Gene: JF781268 / Plasmid: MBP-HTSHP / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H8YRY9

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.55 Å³/Da / Density % sol: 51.68 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 4000, Glycerol, 2-propanol, Sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: BM30A / Wavelength: 0.978196 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 6, 2013

Radiation

Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.978196 Å / Relative weight: 1

Reflection

Resolution: 2.1→49.927 Å / Num. obs: 43867 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / B_iso Wilson estimate: 15.97 Å² / R_merge(I) obs: 0.171 / Χ²: 1.016 / Net I/σ(I): 7.32

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2.1-2.15	0.869	0.634	2.16	10375	3257	2773	0.731	85.1
2.15-2.21	0.93	0.686	2.45	15061	3183	3158	0.77	99.2
2.21-2.28	0.936	0.335	4.81	14696	3072	3057	0.375	99.5
2.28-2.35	0.951	0.543	3.1	14219	2991	2964	0.609	99.1
2.35-2.42	0.957	0.406	3.96	13941	2906	2891	0.455	99.5
2.42-2.51	0.961	0.378	4.25	13731	2842	2829	0.423	99.5
2.51-2.6	0.963	0.333	4.85	13111	2700	2686	0.373	99.5
2.6-2.71	0.979	0.287	5.41	12627	2621	2603	0.322	99.3
2.71-2.83	0.981	0.241	6.3	12158	2521	2511	0.27	99.6
2.83-2.97	0.986	0.213	7.16	11660	2411	2399	0.239	99.5
2.97-3.13	0.992	0.152	8.91	10937	2305	2295	0.17	99.6
3.13-3.32	0.995	0.113	10.65	10202	2188	2175	0.127	99.4
3.32-3.55	0.996	0.104	11.31	9530	2067	2045	0.117	98.9
3.55-3.83	0.995	0.094	13.06	8907	1928	1911	0.106	99.1
3.83-4.2	0.996	0.085	12.77	7957	1771	1748	0.096	98.7
4.2-4.69	0.998	0.063	15.82	7562	1612	1600	0.071	99.3
4.69-5.42	0.998	0.065	15.16	7006	1456	1444	0.073	99.2
5.42-6.64	0.998	0.074	13.02	6028	1240	1236	0.083	99.7
6.64-9.39	0.998	0.069	14	4659	975	972	0.077	99.7
9.39-49.92	0.998	0.055	15.86	2422	602	570	0.063	94.7

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	7.08 Å	49.93 Å
Translation	7.08 Å	49.93 Å

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER	2.5.2	phasing
PHENIX	1.8.2_1309	refinement
PDB_EXTRACT	3.14	data extraction
XDS		data scaling
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.26→49.92 Å / FOM work R set: 0.7444 / SU ML: 0.23 / σ(F): 1.36 / Phase error: 30.59 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.271	1776	5 %
R_work	0.2135	-	-
obs	0.2164	35550	99.16 %

Solvent computation

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

Displacement parameters

B_iso max: 68.89 Å² / B_iso mean: 32.84 Å² / B_iso min: 12.28 Å²

Refinement step

Cycle: LAST / Resolution: 2.26→49.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4738	0	0	403	5141

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	4874
X-RAY DIFFRACTION	f_angle_d	0.893	6669
X-RAY DIFFRACTION	f_chiral_restr	0.06	728
X-RAY DIFFRACTION	f_plane_restr	0.004	887
X-RAY DIFFRACTION	f_dihedral_angle_d	11.717	1727

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.26-2.3211	0.3182	133	0.2687	2556	2689	99
2.3211-2.3894	0.2747	135	0.2445	2549	2684	100
2.3894-2.4665	0.2961	135	0.2375	2557	2692	99
2.4665-2.5547	0.3149	136	0.2365	2587	2723	99
2.5547-2.657	0.2765	134	0.2293	2540	2674	99
2.657-2.7779	0.2645	136	0.2223	2600	2736	99
2.7779-2.9243	0.2973	136	0.2287	2574	2710	99
2.9243-3.1075	0.2625	137	0.2143	2597	2734	100
3.1075-3.3474	0.2878	137	0.2187	2600	2737	99
3.3474-3.6842	0.3415	137	0.2207	2592	2729	99
3.6842-4.2171	0.2571	137	0.1944	2599	2736	99
4.2171-5.3121	0.2079	138	0.1613	2652	2790	99
5.3121-49.9392	0.2001	145	0.1968	2771	2916	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	0.6145	0.1361	0.0771	0.6468	-0.2023	0.4635	-0.0236	0.1143	0.084	-0.0524	0.0006	-0.0001	-0.0819	0.1377	0.0261	0.1587	-0.0025	-0.0087	0.2156	0.1145	0.2108	66.3339	106.5006	127.3762
2	4.7471	-1.9684	1.301	4.7141	-2.0469	0.9873	0.0429	-0.1105	-0.047	0.1359	-0.2921	-0.6949	0.0134	0.4988	0.2592	0.2971	0.0119	-0.0029	0.395	0.193	0.5982	86.2029	108.656	132.5767
3	0.7723	-0.0305	-0.7115	0.8888	-0.1351	0.6489	-0.0032	-0.1004	-0.2513	0.2538	-0.0572	-0.0197	0.0021	0.1598	0.0316	0.2138	-0.0051	0.0096	0.237	0.1055	0.2547	71.5401	91.3068	134.5241
4	1.0657	0.1877	-0.809	1.3843	0.5336	1.3057	0.0358	-0.3324	-0.2602	0.1975	0.2441	-0.2793	0.1413	0.0186	-0.0935	0.2299	0.0363	-0.0537	0.2553	0.1069	0.424	67.3412	82.7434	143.1626
5	0.8599	0.8486	0.4249	1.2925	0.5213	0.7406	-0.0734	0.0639	-0.1513	0.1676	0.3057	-0.2402	0.116	0.1911	0.0876	0.2478	0.0462	-0.012	0.1995	0.2201	0.4129	71.3516	89.9847	140.5752
6	0.2429	-0.1995	-0.2842	0.3673	0.0113	0.6554	-0.2895	-0.358	-0.2324	0.3113	0.0182	-0.1032	0.0445	0.2277	0.1769	0.3574	0.0629	0.0059	0.316	0.1701	0.3311	67.936	88.0943	149.335
7	0.9398	-0.2518	-0.495	1.2968	-0.1862	1.0868	-0.1746	-0.2088	0.0552	0.2529	0.1635	-0.3428	0.1763	0.1212	0.0216	0.2841	0.0298	-0.0786	0.2283	0.0617	0.2388	72.9992	92.5785	145.6159
8	1.1128	1.0188	0.0137	2.015	-1.2926	1.583	0.1195	0.3064	0.0899	0.0225	-0.3769	-0.6499	-0.2494	0.5874	0.1462	0.2203	-0.0328	0.0308	0.3665	0.1297	0.2844	84.2598	108.0484	123.5143
9	0.558	0.1565	-0.2079	1.0622	-0.1522	1.2834	0.0043	-0.0081	0.0866	0.0019	-0.0641	-0.0585	-0.0961	-0.2617	0.0602	0.1645	0.0129	-0.0251	0.2232	0.0806	0.255	69.5206	103.5832	132.5849
10	1.639	0.1361	0.0504	1.0678	-0.1341	1.5942	0.154	-0.133	0.1413	-0.3604	0.0119	-0.1561	-0.2213	-0.0498	-0.0461	0.3044	0.0066	0.0191	0.2408	0.1062	0.2382	72.9094	112.1831	118.2705
11	3.8524	0.4396	0.4094	0.1681	0.2645	0.4339	-0.2227	-0.0406	0.1897	0.1507	-0.1223	-0.2799	-0.4912	0.0899	0.22	0.2421	0.0259	-0.0549	0.2208	0.1101	0.3325	72.1026	118.491	127.916
12	0.0273	-0.0234	-0.0777	0.0232	0.0692	0.2598	-0.0101	0.2645	0.0974	-0.3308	-0.007	-0.0276	0.0358	0.0199	0.1127	0.387	0.0052	0.1535	0.4924	0.2343	0.0482	75.9944	111.0422	113.4647
13	1.1837	0.1016	-0.3174	1.8205	0.2429	0.1224	-0.0856	0.2971	-0.1982	0.0594	0.2146	0.0605	-0.1459	0.0855	-0.0433	0.2361	-0.0164	0.0103	0.1987	0.069	0.2924	54.3182	95.3118	115.7502
14	1.4935	-0.064	0.4757	0.6374	-0.0295	1.3425	-0.1928	0.3315	0.1843	-0.1854	0.2132	0.1384	0.1826	0.3088	-0.0992	0.2738	-0.0104	-0.0554	0.2434	0.093	0.3199	53.9339	92.9948	130.5124
15	1.8327	0.3986	1.486	4.9369	2.8609	5.8952	-0.0139	0.2523	-0.2156	0.1262	0.1143	-0.1884	0.0021	0.377	-0.0886	0.252	0.09	0.0915	0.2281	0.1069	0.4029	54.0535	94.0697	136.5696
16	0.131	0.1558	0.2012	0.5032	0.6759	0.908	-0.1848	-0.2183	-0.0231	0.1165	-0.2172	0.2632	0.2681	0.1205	0.1995	0.2288	0.022	-0.0242	0.2063	0.0836	0.4751	46.537	85.68	131.3118
17	3.6479	-2.3257	-1.2804	2.9977	1.646	0.9568	0.2009	-0.1507	-0.0521	0.5924	0.2617	0.7611	-0.2495	0.0021	-0.2782	0.4264	-0.074	0.0249	0.2989	0.0015	0.628	32.989	90.6528	132.6055
18	2.9959	-1.044	0.7682	2.0506	0.7968	0.8975	0.2896	-0.733	0.0164	-0.1744	-0.0541	-0.1877	0.1927	-0.5296	-0.1939	0.1646	-0.0178	-0.0166	0.2733	0.0622	0.275	36.4772	98.7671	133.6094
19	0.7938	-0.0957	-0.6075	0.0198	0.1349	0.907	-0.1281	0.3212	-0.1147	0.0472	-0.2942	0.2833	-0.2044	0.0235	0.1797	0.2945	0.0352	-0.0294	0.2158	0.0622	0.2412	45.2811	103.9697	123.9104
20	1.5943	0.4136	0.4995	0.148	0.4708	3.1446	0.1115	-0.103	0.0023	-0.0853	-0.0678	0.0743	-0.1684	0.4323	-0.0311	0.2678	-0.0258	-0.0668	0.2111	0.0723	0.2247	51.7659	106.5122	130.5653
21	0.5699	0.2164	0.5076	0.9884	0.252	0.4408	0.0096	-0.1839	-0.0467	0.2305	-0.1159	0.1662	-0.248	-0.1038	0.056	0.3646	0.078	0.0213	0.2655	0.0961	0.2669	51.256	116.1439	146.3177
22	1.4791	0.1504	0.5142	1.1063	0.2886	0.7652	-0.09	-0.151	0.1339	0.2704	0.0575	0.0776	-0.0724	-0.0472	0.0214	0.2732	0.0406	0.0419	0.2521	0.0753	0.1802	48.7193	109.7791	145.3209
23	1.787	1.3702	0.4741	1.8052	1.1472	1.5484	-0.0766	0.1959	-0.3799	-0.0463	-0.205	0.5301	0.118	-0.3596	0.1416	0.131	-0.0031	0.0406	0.3127	0.0448	0.5427	35.0786	91.2306	123.4837
24	0.6667	-0.0667	-0.19	0.1377	0.2201	0.9953	-0.0671	0.0061	-0.1617	0.1562	-0.0107	0.2588	0.1214	-0.0027	0.0611	0.2201	0.0006	0.0037	0.1947	0.0758	0.3194	48.1443	91.9817	126.3976
25	1.0408	-0.1196	-0.1299	0.6915	0.0885	0.1948	-0.0385	0.1352	-0.3083	-0.0452	-0.0216	0.1135	-0.0497	0.07	0.0101	0.3025	0.017	0.0062	0.2852	0.0027	0.4201	44.6598	85.455	118.7397

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A and (resid 225:251 )
2	X-RAY DIFFRACTION	2	chain A and (resid 252:256 )
3	X-RAY DIFFRACTION	3	chain A and (resid 257:296 )
4	X-RAY DIFFRACTION	4	chain A and (resid 327:344 )
5	X-RAY DIFFRACTION	5	chain A and (resid 345:368 )
6	X-RAY DIFFRACTION	6	chain A and (resid 369:402 )
7	X-RAY DIFFRACTION	7	chain A and (resid 403:453 )
8	X-RAY DIFFRACTION	8	chain A and (resid 454:465 )
9	X-RAY DIFFRACTION	9	chain A and (resid 466:507 )
10	X-RAY DIFFRACTION	10	chain A and (resid 508:536 )
11	X-RAY DIFFRACTION	11	chain A and (resid 537:548 )
12	X-RAY DIFFRACTION	12	chain A and (resid 549:565 )
13	X-RAY DIFFRACTION	13	chain B and (resid 225:233 )
14	X-RAY DIFFRACTION	14	chain B and (resid 234:241 )
15	X-RAY DIFFRACTION	15	chain B and (resid 242:246 )
16	X-RAY DIFFRACTION	16	chain B and (resid 247:251 )
17	X-RAY DIFFRACTION	17	chain B and (resid 252:256 )
18	X-RAY DIFFRACTION	18	chain B and (resid 257:261 )
19	X-RAY DIFFRACTION	19	chain B and (resid 262:271 )
20	X-RAY DIFFRACTION	20	chain B and (resid 272:282 )
21	X-RAY DIFFRACTION	21	chain B and (resid 283:296 )
22	X-RAY DIFFRACTION	22	chain B and (resid 327:453 )
23	X-RAY DIFFRACTION	23	chain B and (resid 454:465 )
24	X-RAY DIFFRACTION	24	chain B and (resid 466:536 )
25	X-RAY DIFFRACTION	25	chain B and (resid 537:565 )

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

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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

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

-
Links

-
Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Phasing

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Processing

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About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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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