PDB-8x1h: Crystal structure of N-terminal domain of Nucleocapsid protein of...

ID or keywords:

Entry

Database: PDB / ID: 8x1h

Title

Crystal structure of N-terminal domain of Nucleocapsid protein of SARS-CoV-2

Components

Nucleoprotein

Keywords

RNA BINDING PROTEIN /

Nucleocapsid /

SARS-CoV-2 /

Coronavirus

Function / homology

Function and homology information

cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / RNA stem-loop binding / Maturation of nucleoprotein / positive regulation of NLRP3 inflammasome complex assembly / intracellular non-membrane-bounded organelle / CD28 dependent PI3K/Akt signaling / MHC class I protein binding ...
Similarity search - Function

Biological species

Severe acute respiratory syndrome coronavirus 2

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 2 Å

Authors

Kumari, S. / Gupta, G.D.

Funding support

India, 1items

Citation

Journal: To Be Published
Title: Crystal structure of N-terminal domain of Nucleocapsid protein of SARS-CoV-2
Authors: Kumari, S. / Gupta, G.D.

History

Deposition	Nov 7, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 22, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8x1h.cif.gz	216.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8x1h.ent.gz	174 KB	Display	PDB format
PDBx/mmJSON format	8x1h.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/x1/8x1h ftp://data.pdbj.org/pub/pdb/validation_reports/x1/8x1h	HTTPS FTP

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Related structure data

Similar structure data	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	#245 - May 2020 Spliceosomes similarity (1) #44 - Aug 2003 Calmodulin similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1) #28 - Apr 2002 Anthrax Toxin similarity (1)

Deposited unit

A: Nucleoprotein

B: Nucleoprotein

C: Nucleoprotein

D: Nucleoprotein

hetero molecules

58.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Nucleoprotein

B: Nucleoprotein

C: Nucleoprotein

D: Nucleoprotein

hetero molecules

A: Nucleoprotein

B: Nucleoprotein

C: Nucleoprotein

D: Nucleoprotein

hetero molecules

A: Nucleoprotein

B: Nucleoprotein

C: Nucleoprotein

D: Nucleoprotein

hetero molecules

A: Nucleoprotein

B: Nucleoprotein

C: Nucleoprotein

D: Nucleoprotein

hetero molecules

defined by author
Evidence: gel filtration
235 kDa, 16 polymers

Unit cell

Length a, b, c (Å)	58.945, 92.344, 96.014
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Nucleoprotein / / N / Nucleocapsid protein / NC / Protein N Mass: 14643.348 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Escherichia coli (E. coli) / References: UniProt: P0DTC9
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 45 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 27 % PEG3350, Bicine buffer pH 9.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9778 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 1, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9778 Å / Relative weight: 1
Reflection	Resolution: 2→37.22 Å / Num. obs: 36178 / % possible obs: 100 % / Redundancy: 5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.043 / R_pim(I) all: 0.021 / R_rim(I) all: 0.048 / Χ²: 0.97 / Net I/σ(I): 22.9 / Num. measured all: 182143
Reflection shell	Resolution: 2→2.05 Å / Redundancy: 5.1 % / R_merge(I) obs: 0.478 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2653 / CC_1/2: 0.886 / R_pim(I) all: 0.234 / R_rim(I) all: 0.534 / Χ²: 0.89 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.19.1_4122: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 2→30.24 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.57 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2778	1835	5.08 %	Random selection
R_work	0.2375	-	-	-
obs	0.2396	36104	99.95 %	-

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→30.24 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3914	0	12	210	4136

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	4036
X-RAY DIFFRACTION	f_angle_d	0.549	5495
X-RAY DIFFRACTION	f_dihedral_angle_d	5.227	567
X-RAY DIFFRACTION	f_chiral_restr	0.042	565
X-RAY DIFFRACTION	f_plane_restr	0.005	730

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 (%)
2-2.05	0.3459	147	0.3035	2593	X-RAY DIFFRACTION	100
2.05-2.11	0.3508	137	0.2981	2610	X-RAY DIFFRACTION	100
2.11-2.18	0.358	150	0.2919	2569	X-RAY DIFFRACTION	100
2.18-2.26	0.2895	119	0.2883	2617	X-RAY DIFFRACTION	100
2.26-2.35	0.3307	140	0.2832	2614	X-RAY DIFFRACTION	100
2.35-2.46	0.3192	138	0.2867	2619	X-RAY DIFFRACTION	100
2.46-2.59	0.3296	145	0.2885	2575	X-RAY DIFFRACTION	100
2.59-2.75	0.3469	135	0.2769	2639	X-RAY DIFFRACTION	100
2.75-2.96	0.3153	119	0.2728	2672	X-RAY DIFFRACTION	100
2.96-3.26	0.3126	157	0.2446	2612	X-RAY DIFFRACTION	100
3.26-3.73	0.2761	136	0.2275	2673	X-RAY DIFFRACTION	100
3.73-4.7	0.2231	166	0.1884	2658	X-RAY DIFFRACTION	100
4.7-30.24	0.2233	146	0.1995	2818	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	0.7014	0.5528	0.1425	0.47	0.1011	0.1339	-0.1908	0.0652	-0.2879	0.0602	0.2623	-0.1029	0.366	0.121	0.0323	0.3102	0.0863	-0.0096	0.37	0.0618	0.2326	13.5968	-7.4476	-12.6922
2	0.5607	-0.0724	0.3124	0.36	-0.1278	0.5156	-0.3249	-0.6215	0.0853	0.4452	0.0578	0.0007	-0.2962	-0.2797	-0.0721	0.3165	0.105	-0.0454	0.4836	-0.0083	0.243	8.0879	2.5534	-11.2862
3	0.0332	0.0016	-0.01	0.0043	0.014	0.0454	0.043	0.0704	0.0736	0.1398	0.0139	-0.0463	0.1902	0.1047	-0	0.7243	-0.0152	-0.1308	0.6277	-0.0178	0.9487	19.0892	-25.9244	-9.6326
4	0.1461	0.0311	0.1218	0.0607	-0.0023	0.0907	0.0741	0.1192	-0.402	0.0777	0.1138	0.1115	0.2946	-0.3945	0.0017	0.4087	0.0268	-0.0426	0.3747	0.0413	0.3572	13.4963	-11.5404	-11.1757
5	1.0205	0.5131	0.2687	1.3956	0.4258	0.7208	-0.2489	-0.4551	-0.1902	0.069	0.1989	0.0993	-0.0552	-0.0819	-0.0496	0.1767	0.0847	0.013	0.4454	0.043	0.1835	3.4684	-1.3768	-16.9067
6	0.8128	0.6369	-0.3794	0.5035	-0.3038	0.1801	-0.3585	0.177	0.2014	0.1634	0.1024	-0.1336	-0.2433	-0.0935	-0.2509	0.3514	0.0979	-0.1412	0.4744	-0.0473	0.2261	17.8297	4.2708	-11.8872
7	0.2012	0.2139	0.0541	0.5815	-0.0753	0.0617	-0.0099	-0.2036	-0.0949	-0.0795	-0.1969	-0.1547	0.3274	0.1368	-0.4745	0.7866	0.3733	-0.1675	0.7354	0.0456	0.1491	17.2439	-2.9225	-2.4597
8	1.1226	0.1581	0.6587	0.1786	-0.0281	0.5258	-0.0522	0.374	0.148	-1.0641	-0.3231	-0.4674	-0.3191	0.1111	-0.2726	0.5496	0.0786	0.0715	0.3355	0.0642	0.3307	34.498	-0.3783	6.9389
9	0.0042	0.0271	-0.0089	0.9946	1.01	1.0956	-0.0838	-0.0279	-0.1534	-0.9732	-0.0385	-0.4311	-0.3679	0.2139	-0.2986	0.4222	0.0151	0.1293	0.3368	0.1311	0.38	38.433	2.1349	10.0157
10	0.9955	0.5759	0.9489	0.5954	0.1907	1.633	-0.2238	-0.0582	0.272	-0.8394	-0.2522	0.0583	-0.4087	-0.2494	-1.4644	0.6946	0.085	-0.0308	0.1926	0.1037	0.1621	30.7043	8.4224	6.1831
11	0.1012	-0.041	-0.1353	0.0193	0.051	0.1673	-0.0241	-0.0951	-0.065	-0.2215	-0.0242	0.0268	0.1849	0.1413	-0.0848	0.8113	0.1104	-0.058	0.1325	0.3009	-0.221	30.0266	-9.2266	6.2136
12	0.0358	-0.0162	0.0215	0.035	0.0017	0.0123	0.1278	0.0739	-0.0433	-0.1071	0.1309	-0.4684	0.2482	-0.1801	-0.0005	0.2936	0.0222	-0.0552	0.2784	-0.0269	0.4469	40.1332	-10.1139	28.7575
13	0.037	-0.0341	-0.0394	0.0431	0.0368	0.0346	0.1795	0.2264	-0.5909	-0.0883	0.2773	-0.2203	0.1629	0.0565	0.0021	0.5224	-0.0656	-0.0384	0.5527	-0.0422	0.4954	37.2499	-22.841	17.7407
14	0.0122	0.015	-0.0688	0.0253	-0.0996	0.3863	-0.1699	-0.0037	-0.0016	0.0427	-0.1416	-0.186	0.1189	0.0898	-0.0153	0.4579	0.1824	-0.0953	0.619	-0.2855	1.0994	51.2935	-18.4849	26.8589
15	0.1338	0.1126	-0.1685	0.1303	-0.2526	0.6531	-0.028	-0.2897	-0.197	0.551	0.3566	-1.2443	0.6011	0.4543	0.249	0.4641	0.0666	-0.2527	0.4887	-0.1668	0.7419	44.8566	-18.9012	31.3869
16	0.0283	-0.0013	-0.0028	0.0124	-0.0244	0.0301	0.0931	0.2459	-0.011	-0.359	0.1183	0.7657	-0.0731	-0.4492	-0.0002	0.4266	-0.0632	-0.0836	0.4746	0.0914	0.4209	21.7788	-11.0806	17.9007
17	0.5224	0.0099	-0.2167	0.8576	-0.4955	1.0224	0.116	0.1444	-0.3579	0.4833	0.2648	-0.7698	0.8257	0.0992	0.6554	0.5839	0.0075	-0.1921	0.227	0.0029	0.3563	38.5742	-21.0165	31.7711
18	0.6373	0.7892	-0.5961	1.006	-0.6894	0.6423	0.0007	0.038	-0.0114	0.0896	-0.4308	-0.1838	0.1819	0.0732	-0.5936	1.2503	0.1021	-0.6823	0.6791	-0.0543	0.9785	50.1106	-23.0869	37.5153
19	0.1639	0.2109	0.1957	0.497	0.1382	0.2965	0.0486	0.0294	0.187	0.1623	0.2027	-1.3045	0.22	0.3616	-0.3486	0.3	0.0344	-0.0683	0.2542	-0.132	0.6338	45.1055	-12.4988	24.1512
20	0.1052	-0.1023	-0.0271	0.103	0.0135	0.0654	-0.1339	0.1321	-0.0616	0.1507	-0.191	-0.1813	0.111	-0.105	-0.0711	0.308	-0.1477	-0.0487	0.5581	-0.0009	0.8153	32.1002	-5.6803	-17.2295
21	0.0135	0.0044	-0.0014	0.0021	-0.0007	0.0099	0.055	0.0763	0.1065	0.029	-0.0615	0.1474	0.044	-0.2002	0.0001	0.8732	-0.0357	0.3567	0.8231	0.1639	1.4924	34.0827	-23.5272	-10.2741
22	0.2573	-0.1008	-0.0218	0.1248	-0.0751	0.1256	0.0177	-0.0635	-0.0871	-0.175	0.0057	0.0927	-0.0143	0.0506	-0.0121	0.8112	-0.3267	0.2293	0.587	-0.1009	1.2703	39.7532	-21.0739	-22.5079
23	0.0042	0.0442	0.02	1.0522	0.6445	0.3951	-0.2291	-0.056	-0.9265	-0.2976	-0.0161	0.0432	0.0986	-0.045	-0.0288	0.3833	-0.1744	0.1183	0.6622	-0.1329	1.0801	37.751	-10.2367	-23.6991
24	0.0169	-0.0048	0.0125	0.009	-0.0088	0.0103	-0.0819	0.1539	-0.0341	-0.1141	-0.3458	-0.4006	0.0582	-0.0066	0.0005	0.8185	-0.1484	0.0877	0.8214	0.0963	1.1379	30.0983	-16.6161	0.1333
25	0.6643	0.1419	0.1831	0.2745	0.2436	0.4514	-0.1279	-0.0725	-0.8215	-0.1155	-0.0444	-0.2263	0.3926	-0.1853	-0.5727	0.2604	-0.1972	0.2136	0.2472	0.1061	1.1255	43.0665	-11.5212	-16.2998
26	0.1537	-0.0772	0.1701	0.0648	-0.1684	0.4537	-0.1698	0.1667	0.1784	-0.1827	0.2456	-0.3181	0.0526	-0.1966	0.0871	0.2467	-0.0933	0.0022	0.4703	-0.1372	0.5984	38.358	-3.3495	-23.8263
27	-0.0031	0.0111	-0.0152	0.0912	-0.1012	0.1173	-0.2517	0.208	-0.0672	-0.1425	0.032	-0.0809	0.1413	-0.1098	-0.446	0.3913	-0.2223	0.0856	0.7114	-0.3771	1.0089	28.6781	-14.714	-24.2105
28	0.0104	-0.0053	0.008	0.0047	0.0027	0.0116	-0.0881	-0.0577	-0.1676	-0.06	-0.1639	-0.1608	0.1085	0.0189	0	1.0245	-0.1913	0.1939	0.7425	0.2575	1.611	30.485	-22.9673	-16.8586

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 47 through 63 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 64 through 90 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 91 through 100 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 101 through 112 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 113 through 154 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 155 through 164 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 165 through 174 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 46 through 73 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 74 through 118 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 119 through 159 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 160 through 175 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 48 through 57 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 58 through 67 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 68 through 77 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 78 through 90 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 91 through 106 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 107 through 134 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 135 through 144 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 145 through 174 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 48 through 55 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 56 through 63 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 64 through 73 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 74 through 90 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 91 through 106 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 107 through 134 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 135 through 154 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 155 through 164 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 165 through 174 )

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Yorodumi