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- PDB-9qwi: The N-terminal domain (44-180) of the SARS-CoV-2 nucleocapsid pho... -

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Basic information

Entry
Database: PDB / ID: 9qwi
TitleThe N-terminal domain (44-180) of the SARS-CoV-2 nucleocapsid phosphoprotein using an automatic assignment/modeling software
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / Multidomain protein / Automatic assignment/modeling
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 ...: / 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 / 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
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodSOLUTION NMR / distance geometry
AuthorsSchiavina, M. / Bolognesi, T. / Felli, I.C. / Pierattelli, R.
Funding support Italy, 2items
OrganizationGrant numberCountry
Ministero dell Universita e della RicercaCUP B53C22001790006 Italy
Ministero dell Universita e della Ricerca2021-T4-AN-07 Italy
Citation
Journal: Prog Nucl Magn Reson Spectrosc / Year: 2025
Title: NMR insights on multidomain proteins: the case of the SARS-CoV-2 nucleoprotein.
Authors: Bolognesi, T. / Schiavina, M. / Felli, I.C. / Pierattelli, R.
#1: Journal: Biomol NMR Assign / Year: 2021
Title: The highly flexible disordered regions of the SARS-CoV-2 nucleocapsid N protein within the 1-248 residue construct: sequence-specific resonance assignments through NMR.
Authors: Schiavina, M. / Pontoriero, L. / Uversky, V.N. / Felli, I.C. / Pierattelli, R.
#2: Journal: Biomolecules / Year: 2022
Title: The Role of Disordered Regions in Orchestrating the Properties of Multidomain Proteins: The SARS-CoV-2 Nucleocapsid Protein and Its Interaction with Enoxaparin.
Authors: Schiavina, M. / Pontoriero, L. / Tagliaferro, G. / Pierattelli, R. / Felli, I.C.
History
DepositionApr 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)14,8711
Polymers14,8711
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

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


Mass: 14870.526 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
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 13C CACO
131isotropic12D 13C CBCACO
141isotropic12D 13C CON
151isotropic12D 1H-15N HSQC
161isotropic13D HNCO
171isotropic13D 13C (H)CBCACON

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Sample preparation

DetailsType: solution
Contents: 450 uM [U-100% 13C; U-100% 15N] NTD (44-180) of N protein from SARS-CoV-2, 0.03 % NaN3, 150 mM KCl, 95 % H2O, 5 % [U-2H] D2O, 95% H2O/5% D2O
Label: sample_1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
450 uMNTD (44-180) of N protein from SARS-CoV-2[U-100% 13C; U-100% 15N]1
0.03 %NaN3natural abundance1
150 mMKClnatural abundance1
95 %H2Onatural abundance1
5 %D2O[U-2H]1
Sample conditionsIonic strength: 170 mM / Label: sample_conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 950 MHz
Details: Bruker AVANCE III spectrometer operating at 950.20 MHz 1H, 238.93 MHz 13C and 96.28 15N MHz frequencies equipped with a cryogenically cooled probehead optimized for 1H-direct detection (TCI).

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Processing

NMR software
NameDeveloperClassification
ARTINAKlukowski, P., Riek, R. and Guntert, P.chemical shift assignment
ARTINAKlukowski, P., Riek, R. and Guntert, P.structure calculation
ARTINAKlukowski, P., Riek, R. and Guntert, P.peak picking
XEASYBartels et al.chemical shift assignment
RefinementMethod: distance geometry / Software ordinal: 3
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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