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- PDB-9fbg: SARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant P151S -

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Basic information

Entry
Database: PDB / ID: 9fbg
TitleSARS-CoV-2 Nucleocapsid N-terminal domain (NTD) mutant P151S
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Nucelocapsid / N-terminal domain / Omicron BA. 4
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 / SARS-CoV-2 targets host intracellular signalling and regulatory pathways ...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 / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein sequestering activity / VEGFR2 mediated vascular permeability / molecular condensate scaffold activity / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / DDX58/IFIH1-mediated induction of interferon-alpha/beta / MHC class I protein complex / RNA stem-loop binding / Interleukin-1 signaling / Interferon alpha/beta signaling / viral capsid / PIP3 activates AKT signaling / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / viral nucleocapsid / host cell Golgi apparatus / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / Induction of Cell-Cell Fusion / Attachment and Entry / host cell perinuclear region of cytoplasm / ribonucleoprotein complex / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / RNA binding / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
Nucleocapsid protein, betacoronavirus / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile.
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsDhamotharan, K. / Schlundt, A.
Funding support Germany, 4items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHL2062/2-1 and 2-2 Germany
German Research Foundation (DFG)161793742 Germany
Other governmentGoethe-Corona-Funds
Other governmentJohanna Quandt Young Academy at Goethe (stipend number 2019/AS01)
CitationJournal: 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
DepositionMay 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
E: Nucleoprotein
F: Nucleoprotein
G: Nucleoprotein
H: Nucleoprotein
I: Nucleoprotein
J: Nucleoprotein
K: Nucleoprotein
L: Nucleoprotein
M: Nucleoprotein
N: Nucleoprotein
O: Nucleoprotein
P: Nucleoprotein
Q: Nucleoprotein
R: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)267,92218
Polymers267,92218
Non-polymers00
Water20,1051116
1
A: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8851
Polymers14,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8851
Polymers14,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8851
Polymers14,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8851
Polymers14,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8851
Polymers14,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8851
Polymers14,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8851
Polymers14,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8851
Polymers14,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8851
Polymers14,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8851
Polymers14,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8851
Polymers14,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8851
Polymers14,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8851
Polymers14,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8851
Polymers14,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
O: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8851
Polymers14,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
P: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8851
Polymers14,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
17
Q: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8851
Polymers14,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
18
R: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8851
Polymers14,8851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)188.111, 108.883, 146.272
Angle α, β, γ (deg.)90, 100.79, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Nucleoprotein / N / Nucleocapsid protein / NC / Protein N


Mass: 14884.554 Da / Num. of mol.: 18 / Mutation: P151S
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.: 1116 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100mM Sodium HEPES pH 7.5 4.3M Sodium chloride / PH range: 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.54→47.9 Å / Num. obs: 95472 / % possible obs: 99.8 % / Redundancy: 3.5 % / CC1/2: 0.998 / Χ2: 1.04 / Net I/σ(I): 11.7
Reflection shellResolution: 2.54→2.58 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4703 / CC1/2: 0.675 / Χ2: 1.04

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
REFMAC5.8.0425refinement
PDB-REDO8.06refinement
Coot0.9.8.8model building
BUCCANEER3.5.2model building
Aimless0.7.13data scaling
pointless1.12.15data scaling
STARANISO2.3.74data scaling
autoPROC1.1.7data reduction
XDSBUILT 20230630data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→47.75 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.891 / SU R Cruickshank DPI: 0.604 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.615 / SU Rfree Blow DPI: 0.296 / SU Rfree Cruickshank DPI: 0.3
RfactorNum. reflection% reflectionSelection details
Rfree0.2605 4743 -RANDOM
Rwork0.2208 ---
obs0.2228 95468 99.8 %-
Displacement parametersBiso mean: 60.74 Å2
Baniso -1Baniso -2Baniso -3
1-2.7051 Å20 Å26.703 Å2
2--12.9012 Å20 Å2
3----15.6063 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.54→47.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18516 0 0 1116 19632
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00719034HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.7925881HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6304SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes3270HARMONIC5
X-RAY DIFFRACTIONt_it19034HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion2402SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact14065SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion16.06
LS refinement shellResolution: 2.54→2.56 Å
RfactorNum. reflection% reflection
Rfree0.3853 88 -
Rwork0.3067 --
obs0.3104 1910 99.69 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
14.76190.2144-0.07245.93590.72434.61690.09960.0441-0.45480.0441-0.1518-0.1015-0.4548-0.10150.05220.12-0.0694-0.02730.1724-0.02340.1548-9.466227.33465.6278
25.59810.10490.99916.05690.95843.4879-0.0485-0.2958-0.3547-0.2958-0.00440.0663-0.35470.06630.0530.01840.0589-0.0140.0075-0.02950.103831.626312.341553.3833
36.07750.26841.07825.71440.68443.8505-0.0588-0.0806-0.2981-0.08060.00720.3084-0.29810.30840.05160.12410.0495-0.03150.2510.01790.232229.078115.82245.2688
45.9038-0.0668-1.11755.489-0.64814.1562-0.1061-0.1805-0.1457-0.18050.02140.4457-0.14570.44570.08470.25620.0090.00570.08080.03730.268738.2752-0.4676-5.3029
56.3556-0.8812-0.08986.46910.99614.2991-0.0248-0.109-0.2551-0.109-0.0119-0.2585-0.2551-0.25850.0367-0.0531-0.012-0.00450.0406-0.00890.2295-5.156327.548353.4819
65.6606-0.3294-0.74665.72780.66893.3912-0.0549-0.26710.1377-0.2671-0.00710.4760.13770.4760.0620.16230.03160.01290.0266-0.01770.18439.4585-5.275442.8507
75.48160.13190.63025.2878-1.04483.6341-0.0207-0.12490.1267-0.1249-0.04030.25450.12670.25450.061-0.0451-0.0039-0.03390.0336-0.02940.12615.467456.957452.994
84.07520.03550.65844.1832-0.05693.6204-0.0374-0.36850.4108-0.3685-0.00280.00430.41080.00430.04030.0558-0.04760.00650.0372-0.03620.134425.506166.092242.6762
96.63850.14121.40135.53480.35163.4007-0.09450.0185-0.08530.0185-0.0022-0.3295-0.0853-0.32950.09670.10630.0201-0.0394-0.01180.03730.12729.941227.453590.6225
106.4849-0.4601-1.28625.59270.15173.5664-0.17110.06780.07360.0678-0.0075-0.22430.0736-0.22430.17860.0949-0.0189-0.0395-0.0080.02230.289957.065157.376853.3428
115.22410.57-1.03975.5208-0.6443.71880.0363-0.16820.3247-0.1682-0.0953-0.02440.3247-0.02440.05910.05040.0493-0.01610.00360.03330.319662.783717.699453.3089
126.13060.514-0.18136.2546-0.0753.7672-0.0179-0.14220.3552-0.14220.0119-0.34660.3552-0.34660.00590.18290.06660.07450.2776-0.00380.313164.945714.70245.4838
135.76890.0262-0.35876.0223-0.45694.31540.0544-0.3471-0.407-0.3471-0.07030.3065-0.4070.30650.01590.04950.07-0.00920.10890.00650.204813.589125.223242.2119
146.07280.69330.74875.38980.19494.057-0.0262-0.24860.2692-0.2486-0.0237-0.25680.2692-0.25680.04990.0460.0673-0.04440.1051-0.03190.1911-13.662758.835342.7572
155.9424-0.49830.76645.8422-0.08424.2141-0.0663-0.0822-0.1848-0.0822-0.1353-0.419-0.1848-0.4190.20160.19080.015-0.0350.0321-0.00980.317254.564835.475543.173
165.028-0.17370.2586.1828-0.68173.80670.14690.22090.42530.2209-0.21160.09530.42530.09530.06470.2236-0.0920.06240.24490.0120.34199.62958.09325.2343
176.29910.29020.59576.0394-0.08264.1698-0.1286-0.19890.2168-0.19890.1404-0.46020.2168-0.4602-0.01180.2931-0.0352-0.00150.1088-0.04920.288655.330631.1527-5.3488
185.8451-0.02270.69046.1842-0.74573.8824-0.19220.0302-0.47550.03020.0522-0.2251-0.4755-0.22510.140.1118-0.0612-0.09190.14130.05020.4375-25.968118.485142.9929
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|42 - A|174 }A42 - 174
2X-RAY DIFFRACTION2{ B|42 - B|174 }B42 - 174
3X-RAY DIFFRACTION3{ C|41 - C|172 }C41 - 172
4X-RAY DIFFRACTION4{ D|41 - D|171 }D41 - 171
5X-RAY DIFFRACTION5{ E|42 - E|171 }E42 - 171
6X-RAY DIFFRACTION6{ F|41 - F|174 }F41 - 174
7X-RAY DIFFRACTION7{ G|41 - G|172 }G41 - 172
8X-RAY DIFFRACTION8{ H|41 - H|174 }H41 - 174
9X-RAY DIFFRACTION9{ I|41 - I|174 }I41 - 174
10X-RAY DIFFRACTION10{ J|41 - J|172 }J41 - 172
11X-RAY DIFFRACTION11{ K|41 - K|174 }K41 - 174
12X-RAY DIFFRACTION12{ L|42 - L|174 }L42 - 174
13X-RAY DIFFRACTION13{ M|42 - M|174 }M42 - 174
14X-RAY DIFFRACTION14{ N|42 - N|172 }N42 - 172
15X-RAY DIFFRACTION15{ O|41 - O|174 }O41 - 174
16X-RAY DIFFRACTION16{ P|41 - P|174 }P41 - 174
17X-RAY DIFFRACTION17{ Q|42 - Q|172 }Q42 - 172
18X-RAY DIFFRACTION18{ R|41 - R|172 }R41 - 172

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