PDB-9f83: SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant D63G

ID or keywords:

Entry

Database: PDB / ID: 9f83

Title

SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant D63G

Components

Nucleoprotein

Keywords

VIRAL PROTEIN / SARS-CoV-2 / Nucleocapsid / N-terminal domain / Delta variant

Function / homology

Function and homology information

: / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / poly(U) RNA binding / Maturation of nucleoprotein / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / CD28 dependent PI3K/Akt signaling ...
Similarity search - Function

Biological species

Severe acute respiratory syndrome coronavirus 2

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Dhamotharan, K. / Schlundt, A. / Guenther, S.

Funding support

Germany, 4items

Organization	Grant number	Country
German Research Foundation (DFG)	SCHL2062/2-1 and 2-2	Germany
German Research Foundation (DFG)	161793742	Germany
Other government	Goethe-Corona-Funds
Other government	Johanna Quandt Young Academy at Goethe (stipend number 2019/AS01)

Citation

Journal: Nat Commun / Year: 2024
Title: A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.
Authors: Dhamotharan, K. / Korn, S.M. / Wacker, A. / Becker, M.A. / Gunther, S. / Schwalbe, H. / Schlundt, A.

History

Deposition	May 6, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 20, 2024	Provider: repository / Type: Initial release
Revision 1.1	Dec 18, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9f83.cif.gz	207 KB	Display	PDBx/mmCIF format
PDB format	pdb9f83.ent.gz	162.7 KB	Display	PDB format
PDBx/mmJSON format	9f83.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	9f83_validation.pdf.gz	460.2 KB	Display	wwPDB validaton report
Full document	9f83_full_validation.pdf.gz	468.9 KB	Display
Data in XML	9f83_validation.xml.gz	29.8 KB	Display
Data in CIF	9f83_validation.cif.gz	40.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f8/9f83 ftp://data.pdbj.org/pub/pdb/validation_reports/f8/9f83	HTTPS FTP

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Related structure data

Related structure data	9evyC 9ewhC 9exbC 9ezbC 9f5jC 9f5lC 9f7aC 9f7cC 9fbgC C: citing same article (ref.)
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

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

1

A: Nucleoprotein

defined by author
Evidence: gel filtration
14.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Nucleoprotein

defined by author
14.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Nucleoprotein

defined by author
14.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Nucleoprotein

defined by author
14.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	59.013, 55.665, 84.895
Angle α, β, γ (deg.)	90, 95.148, 90
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	GLY	GLY	50 - 170	12 - 132
2	1	1	GLY	GLY	50 - 170	12 - 132
3	2	2	LEU	LEU	50 - 167	12 - 129
4	2	2	LEU	LEU	50 - 167	12 - 129
5	3	3	GLY	GLY	50 - 170	12 - 132
6	3	3	GLY	GLY	50 - 170	12 - 132
7	4	4	LEU	LEU	50 - 167	12 - 129
8	4	4	LEU	LEU	50 - 167	12 - 129
9	5	5	PHE	PHE	50 - 171	12 - 133
10	5	5	PHE	PHE	50 - 171	12 - 133
11	6	6	LEU	LEU	50 - 167	12 - 129
12	6	6	LEU	LEU	50 - 167	12 - 129

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	Nucleoprotein / N / Nucleocapsid protein / NC / Protein N Mass: 14836.554 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 BL21(DE3) (bacteria) / References: UniProt: P0DTC9
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.35 Å³/Da / Density % sol: 47.6 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 50mM HEPES pH 6.8 150mM Sodium Chloride 24% PEG 3350 2% PEG 400

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

PETRA III, EMBL c/o DESY

/ Beamline: P13 (MX1) / Wavelength: 0.976 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2023

Radiation

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

Radiation wavelength

Wavelength: 0.976 Å / Relative weight: 1

Reflection

Resolution: 1.7→84.55 Å / Num. obs: 59866 / % possible obs: 98.9 % / Redundancy: 6.6 % / CC_1/2: 0.998 / R_merge(I) obs: 0.078 / R_pim(I) all: 0.049 / R_rim(I) all: 0.093 / Net I/σ(I): 12.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
9-84.55	6	0.049	440	0.994	0.032	0.058
1.7-1.73	6.8	1.101	3151	0.736	0.688	1.303

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
BUSTER	2.10.4	refinement
Coot	0.9.8.8	model building
BUCCANEER	3.5.2	model building
Aimless	0.7.13	data scaling
pointless	1.12.15	data scaling
STARANISO	2.3.74	data scaling
autoPROC	1.17	data reduction
XDS	BUILT 20230630	data reduction
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.7→50.479 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.928 / SU B: 3.754 / SU ML: 0.117 / Cross valid method: FREE R-VALUE / ESU R: 0.134 / ESU R Free: 0.136
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2802	2793	4.787 %
R_work	0.2291	55554	-
all	0.232	-	-
obs	-	58347	96.354 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 41.319 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.986 Å²	0 Å²	-0.312 Å²
2-	-	0.731 Å²	-0 Å²
3-	-	-	1.29 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→50.479 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3794	0	0	502	4296

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.012	3903
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	3626
X-RAY DIFFRACTION	r_angle_refined_deg	2.083	1.823	5307
X-RAY DIFFRACTION	r_angle_other_deg	0.782	1.768	8336
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.936	5	485
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	11.104	5	32
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.57	10	591
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.513	10	178
X-RAY DIFFRACTION	r_chiral_restr	0.11	0.2	538
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.02	4792
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	968
X-RAY DIFFRACTION	r_nbd_refined	0.194	0.2	664
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.164	0.2	3108
X-RAY DIFFRACTION	r_nbtor_refined	0.175	0.2	1827
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	2088
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.181	0.2	367
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.112	0.2	6
X-RAY DIFFRACTION	r_nbd_other	0.121	0.2	44
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.228	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	34.72	3.721	1952
X-RAY DIFFRACTION	r_mcbond_other	34.72	3.72	1952
X-RAY DIFFRACTION	r_mcangle_it	27.5	6.578	2433
X-RAY DIFFRACTION	r_mcangle_other	27.495	6.578	2434
X-RAY DIFFRACTION	r_scbond_it	42.49	4.286	1951
X-RAY DIFFRACTION	r_scbond_other	42.511	4.283	1949
X-RAY DIFFRACTION	r_scangle_it	38.383	7.304	2874
X-RAY DIFFRACTION	r_scangle_other	38.377	7.306	2875
X-RAY DIFFRACTION	r_lrange_it	34.447	36.498	4400
X-RAY DIFFRACTION	r_lrange_other	34.911	35.719	4275
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.087	0.05	3582
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.122	0.05	3391
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.103	0.05	3552
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.138	0.05	3313
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.115	0.05	3580
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.127	0.05	3425

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.08711	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.08711	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.12245	0.05008
2	4	A	X-RAY DIFFRACTION	Local ncs	0.12245	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.10268	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.10268	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.13829	0.05008
4	8	A	X-RAY DIFFRACTION	Local ncs	0.13829	0.05008
5	9	A	X-RAY DIFFRACTION	Local ncs	0.11488	0.05008
5	10	A	X-RAY DIFFRACTION	Local ncs	0.11488	0.05008
6	11	A	X-RAY DIFFRACTION	Local ncs	0.12743	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.12743	0.05009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.7-1.744	0.332	249	0.319	4150	0.32	4442	0.915	0.921	99.032	0.297
1.744-1.792	0.346	220	0.295	4068	0.298	4339	0.918	0.935	98.8246	0.272
1.792-1.844	0.311	194	0.283	3943	0.285	4247	0.923	0.94	97.4099	0.257
1.844-1.9	0.416	204	0.371	3671	0.374	4060	0.885	0.905	95.4434	0.353
1.9-1.963	0.608	151	0.574	2813	0.576	3969	0.682	0.716	74.6788	0.563
1.963-2.031	0.312	179	0.262	3693	0.264	3883	0.94	0.956	99.7167	0.241
2.031-2.108	0.304	182	0.215	3495	0.219	3691	0.941	0.97	99.6207	0.196
2.108-2.194	0.281	140	0.215	3412	0.218	3560	0.95	0.969	99.7753	0.198
2.194-2.291	0.457	140	0.42	2884	0.422	3450	0.805	0.829	87.6522	0.366
2.291-2.403	0.31	118	0.213	3138	0.216	3262	0.95	0.97	99.8161	0.195
2.403-2.533	0.284	139	0.196	3000	0.2	3147	0.958	0.978	99.7458	0.189
2.533-2.686	0.254	127	0.204	2820	0.206	2955	0.952	0.975	99.7293	0.198
2.686-2.871	0.295	149	0.202	2603	0.207	2765	0.948	0.975	99.5298	0.205
2.871-3.1	0.253	130	0.19	2477	0.194	2624	0.964	0.978	99.3521	0.197
3.1-3.394	0.265	112	0.211	2199	0.213	2384	0.961	0.975	96.9379	0.222
3.394-3.793	0.229	71	0.199	1882	0.2	2170	0.966	0.979	90	0.21
3.793-4.375	0.222	124	0.161	1802	0.165	1926	0.973	0.986	100	0.181
4.375-5.349	0.172	76	0.148	1572	0.15	1649	0.986	0.988	99.9394	0.176
5.349-7.522	0.213	43	0.158	1232	0.16	1275	0.971	0.986	100	0.185
7.522-50.479	0.197	45	0.194	700	0.194	755	0.977	0.973	98.6755	0.227

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