PDB-9f7c: SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant S105I

ID or keywords:

Entry

Database: PDB / ID: 9f7c

Title

SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant S105I

Components

Nucleoprotein

Keywords

VIRAL PROTEIN / SARS-CoV-2 / Nucelocapsid / N-terminal domain

Function / homology

Function and homology information

: / response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / Maturation of nucleoprotein / poly(U) RNA binding / 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 /

SAD / Resolution: 2 Å

Authors

Dhamotharan, K. / Schlundt, A.

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 3, 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

-
Download

PDBx/mmCIF format	9f7c.cif.gz	137.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9f7c.ent.gz	91.1 KB	Display	PDB format
PDBx/mmJSON format	9f7c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9f7c_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	9f7c_full_validation.pdf.gz	1.3 MB	Display
Data in XML	9f7c_validation.xml.gz	8.9 KB	Display
Data in CIF	9f7c_validation.cif.gz	11 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f7/9f7c ftp://data.pdbj.org/pub/pdb/validation_reports/f7/9f7c	HTTPS FTP

-
Related structure data

Related structure data	9evyC 9ewhC 9exbC 9ezbC 9f5jC 9f5lC 9f7aC 9f83C 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

-
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

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	58.616, 58.616, 111.588
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	92
Space group name H-M	P4₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-201- ZN

#1: Protein	Nucleoprotein Mass: 14920.671 Da / Num. of mol.: 1 / Mutation: S105I 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: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.22 Å³/Da / Density % sol: 61.82 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 22% PEG 3350 200mM Zinc Acetate dihydrate

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→41.45 Å / Num. obs: 13840 / % possible obs: 99.3 % / Redundancy: 12.4 % / CC_1/2: 0.999 / Χ²: 0.95 / Net I/σ(I): 15.8
Reflection shell	Resolution: 2→2.05 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 921 / CC_1/2: 0.938 / Χ²: 0.89

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.88)	refinement
REFMAC	5.8.0430 (refmacat 0.4.88)	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	1.1.7	data reduction
XDS	BUILT 20230630	data reduction
CRANK2	2.0.339	phasing

Refinement

Method to determine structure:

SAD / Resolution: 2→41.45 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.943 / WR_factor R_free: 0.288 / WR_factor R_work: 0.253 / SU B: 10.743 / SU ML: 0.15 / Average fsc free: 0.9104 / Average fsc overall: 0.9401 / Average fsc work: 0.9416 / Cross valid method: FREE R-VALUE / ESU R: 0.175 / ESU R Free: 0.161
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2733	685	4.978 %	RANDOM
R_work	0.2411	13075	-	-
all	0.243	-	-	-
obs	-	13760	99.761 %	-

Solvent computation

Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 81.96 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.817 Å²	-0 Å²	0 Å²
2-	-	2.817 Å²	0 Å²
3-	-	-	-5.633 Å²

Refinement step

Cycle: LAST / Resolution: 2→41.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1046	0	2	52	1100

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	1079
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	1000
X-RAY DIFFRACTION	r_ext_dist_refined_b	0	0.01	3669
X-RAY DIFFRACTION	r_angle_refined_deg	2.561	1.817	1469
X-RAY DIFFRACTION	r_angle_other_deg	0.88	1.772	2299
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.716	5	133
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.173	5	9
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.337	10	163
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.137	10	51
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	149
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1324
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	266
X-RAY DIFFRACTION	r_nbd_refined	0.199	0.2	132
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.169	0.2	834
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.2	487
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	575
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.126	0.2	39
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.337	0.2	22
X-RAY DIFFRACTION	r_nbd_other	0.178	0.2	40
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.105	0.2	4
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.075	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	4.78	5.673	535
X-RAY DIFFRACTION	r_mcbond_other	4.779	5.672	535
X-RAY DIFFRACTION	r_mcangle_it	6.427	10.212	667
X-RAY DIFFRACTION	r_mcangle_other	6.423	10.207	668
X-RAY DIFFRACTION	r_scbond_it	6.049	5.962	544
X-RAY DIFFRACTION	r_scbond_other	6.047	5.969	542
X-RAY DIFFRACTION	r_scangle_it	7.983	10.803	802
X-RAY DIFFRACTION	r_scangle_other	7.978	10.798	803
X-RAY DIFFRACTION	r_lrange_it	10.054	68.248	4131
X-RAY DIFFRACTION	r_lrange_other	10.054	68.183	4109

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
2-2.052	0.382	41	0.365	914	0.365	978	0.872	0.862	97.6483	0.344
2.052-2.108	0.434	52	0.323	932	0.328	984	0.843	0.888	100	0.29
2.108-2.169	0.39	50	0.324	889	0.328	940	0.888	0.908	99.8936	0.303
2.169-2.235	0.293	40	0.278	872	0.278	912	0.946	0.934	100	0.25
2.235-2.308	0.27	47	0.301	831	0.299	881	0.956	0.928	99.6595	0.266
2.308-2.389	0.281	48	0.267	820	0.268	869	0.942	0.952	99.8849	0.236
2.389-2.479	0.351	36	0.282	796	0.285	834	0.923	0.949	99.7602	0.256
2.479-2.58	0.236	45	0.247	753	0.246	798	0.96	0.962	100	0.228
2.58-2.694	0.376	44	0.248	737	0.254	781	0.936	0.964	100	0.228
2.694-2.825	0.269	31	0.241	713	0.242	744	0.961	0.964	100	0.221
2.825-2.977	0.262	23	0.251	685	0.251	708	0.952	0.961	100	0.242
2.977-3.157	0.322	35	0.242	639	0.247	675	0.945	0.963	99.8519	0.243
3.157-3.373	0.281	39	0.266	603	0.267	642	0.958	0.957	100	0.268
3.373-3.642	0.231	38	0.249	559	0.248	597	0.964	0.965	100	0.252
3.642-3.986	0.332	27	0.233	532	0.238	559	0.935	0.969	100	0.242
3.986-4.451	0.19	26	0.195	482	0.194	508	0.98	0.976	100	0.221
4.451-5.13	0.271	20	0.186	430	0.189	450	0.958	0.976	100	0.214
5.13-6.259	0.248	18	0.225	380	0.226	398	0.968	0.968	100	0.28
6.259-8.753	0.239	12	0.257	310	0.257	322	0.947	0.953	100	0.302
8.753-41.45	0.28	13	0.281	196	0.281	210		0.946	99.5238	0.351

Refinement TLS params.

Method: refined / Origin x: 32.4779 Å / Origin y: 10.936 Å / Origin z: 17.8841 Å

	11	12	13	21	22	23	31	32	33
T	0.0732 Å²	-0.0085 Å²	0.0393 Å²	-	0.0447 Å²	0.0253 Å²	-	-	0.0426 Å²
L	3.7488 °²	0.1273 °²	-0.8268 °²	-	5.8488 °²	1.8284 °²	-	-	5.363 °²
S	0.0026 Å °	-0.2411 Å °	-0.2079 Å °	-0.1629 Å °	-0.0345 Å °	-0.0818 Å °	0.2794 Å °	-0.2881 Å °	0.0319 Å °

Refinement TLS group

Selection: ALL

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi