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- PDB-9kn1: Crystal structure of SARS-CoV-2 nucleocapsid phosphoprotein N-ter... -

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Basic information

Entry
Database: PDB / ID: 9kn1
TitleCrystal structure of SARS-CoV-2 nucleocapsid phosphoprotein N-terminal domain(N-NTD) in complex with UMP
Components(Nucleoprotein) x 4
KeywordsVIRAL PROTEIN / SARS-CoV-2 / nucleocapsid / nucleic acid binding protein
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 ...: / 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 / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein sequestering activity / VEGFR2 mediated vascular permeability / molecular condensate scaffold activity / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / 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 / viral nucleocapsid / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / Translation of Structural Proteins / Virion Assembly and Release / host extracellular space / host cell Golgi apparatus / 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
PHOSPHATE ION / URIDINE-5'-MONOPHOSPHATE / Nucleoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsHigashiura, A. / Yamamoto, A. / Ito, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Virology / Year: 2025
Title: Structural insights into nucleocapsid protein variability: Implications for PJ34 efficacy against SARS-CoV-2.
Authors: Yamamoto, A. / Ito, H. / Sakaguchi, T. / Higashiura, A.
History
DepositionNov 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0926
Polymers55,6734
Non-polymers4192
Water4,738263
1
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0682
Polymers13,7431
Non-polymers3241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7620 Å2
MethodPISA
2
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1962
Polymers14,1011
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-5 kcal/mol
Surface area7840 Å2
MethodPISA
3
C: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)13,9721
Polymers13,9721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7820 Å2
MethodPISA
4
D: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)13,8571
Polymers13,8571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.753, 92.659, 97.412
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 4 types, 4 molecules ABCD

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


Mass: 13743.378 Da / Num. of mol.: 1 / Fragment: N-terminal domain
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: Protein Nucleoprotein / N / Nucleocapsid protein / NC / Protein N


Mass: 14100.698 Da / Num. of mol.: 1
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
#3: Protein Nucleoprotein / N / Nucleocapsid protein / NC / Protein N


Mass: 13971.584 Da / Num. of mol.: 1
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
#4: Protein Nucleoprotein / N / Nucleocapsid protein / NC / Protein N


Mass: 13857.481 Da / Num. of mol.: 1
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

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Non-polymers , 3 types, 265 molecules

#5: Chemical ChemComp-U / URIDINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.33 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 30% PEG3350, 100 mM Tris-HCl pH8.0, 5 mM UMP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.12→48.71 Å / Num. obs: 30878 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 40.6 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.155 / Net I/σ(I): 7.7
Reflection shellResolution: 2.12→2.18 Å / Num. unique obs: 2480 / CC1/2: 0.439 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→48.71 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2928 1449 4.71 %
Rwork0.2243 --
obs0.2275 30735 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.12→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3937 0 26 263 4226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.881
X-RAY DIFFRACTIONf_dihedral_angle_d14.561492
X-RAY DIFFRACTIONf_chiral_restr0.051567
X-RAY DIFFRACTIONf_plane_restr0.009733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.20.38631510.33522801X-RAY DIFFRACTION97
2.2-2.280.36131410.32242881X-RAY DIFFRACTION99
2.28-2.390.39341450.31952883X-RAY DIFFRACTION100
2.39-2.510.38231560.30522888X-RAY DIFFRACTION100
2.51-2.670.391680.29162907X-RAY DIFFRACTION100
2.67-2.880.34891440.28872904X-RAY DIFFRACTION100
2.88-3.170.27471380.24922920X-RAY DIFFRACTION100
3.17-3.620.34031270.21992976X-RAY DIFFRACTION100
3.62-4.570.28051390.17592994X-RAY DIFFRACTION100
4.57-48.710.18831400.17173132X-RAY DIFFRACTION100

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