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- PDB-9cj6: Crystal Structure of SARS-CoV-2 N-NTD with part of N-arm complex ... -

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Basic information

Entry
Database: PDB / ID: 9cj6
TitleCrystal Structure of SARS-CoV-2 N-NTD with part of N-arm complex with ssDNA.
Components
  • DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • Nucleoprotein
KeywordsVIRAL PROTEIN/DNA / STRUCTURAL PROTEIN / VIRAL PROTEIN / Nucleocapsid / PROTEIN-DNA complex / VIRAL PROTEIN-DNA complex
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
DNA / DNA (> 10) / Nucleoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMaiti, A. / Matsuo, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)under contract 75N91019D00024 United States
CitationJournal: Biomolecules / Year: 2024
Title: Affinity Tag-Free Purification of SARS-CoV-2 N Protein and Its Crystal Structure in Complex with ssDNA.
Authors: Maiti, A. / Matsuo, H.
History
DepositionJul 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
B: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)51,7292
Polymers51,7292
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.891, 90.891, 36.341
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

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


Mass: 45689.645 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
#2: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 6038.899 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 1.64 Å3/Da / Density % sol: 25.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.2M HEPES, pH 7.4 + 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 21606 / % possible obs: 99.8 % / Redundancy: 12.9 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.019 / Rrim(I) all: 0.07 / Χ2: 0.958 / Net I/σ(I): 10.8 / Num. measured all: 278517
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.55-1.6111.60.65320970.9450.9860.1860.680.66698.6
1.61-1.6712.80.49921550.9690.9920.140.5180.748100
1.67-1.75130.33621750.9810.9950.0950.3490.84100
1.75-1.8411.90.24621110.9870.9970.0740.2570.90899.9
1.84-1.9513.60.17821680.9930.9980.0490.1841.285100
1.95-2.113.70.13321580.9950.9990.0370.1381.088100
2.1-2.3213.40.10121510.9970.9990.0280.1051.03100
2.32-2.6512.30.07821800.9970.9990.0230.0810.82399.9
2.65-3.3413.70.05621890.9980.9990.0160.0580.949100
3.34-5012.80.0422220.99910.0120.0421.16299.4

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→33.74 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2044 1050 5 %
Rwork0.179 --
obs0.1804 20986 96.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→33.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1042 44 0 177 1263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d13.854419
X-RAY DIFFRACTIONf_chiral_restr0.057159
X-RAY DIFFRACTIONf_plane_restr0.008201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.620.3015920.24512049X-RAY DIFFRACTION80
1.62-1.710.25111230.21512460X-RAY DIFFRACTION96
1.71-1.820.27991340.21292550X-RAY DIFFRACTION100
1.82-1.960.26761490.20472532X-RAY DIFFRACTION100
1.96-2.150.21491500.18992564X-RAY DIFFRACTION100
2.15-2.470.19251280.16582562X-RAY DIFFRACTION100
2.47-3.10.14621040.17772600X-RAY DIFFRACTION100
3.11-33.740.18741700.15352619X-RAY DIFFRACTION100

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