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- PDB-7sd4: SARS-CoV-2 Nucleocapsid N-terminal domain (N-NTD) protein -

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Basic information

Entry
Database: PDB / ID: 7sd4
TitleSARS-CoV-2 Nucleocapsid N-terminal domain (N-NTD) protein
ComponentsNucleoprotein
KeywordsSTRUCTURAL PROTEIN / COVID-19 / SARS-CoV-2 / nucleocapsid protein / N-terminal domain / RNA-binding domain
Function / homology
Function and homology information


cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / Maturation of nucleoprotein / intracellular non-membrane-bounded 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 ...cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / Maturation of nucleoprotein / intracellular non-membrane-bounded 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 / Interleukin-1 signaling / RNA stem-loop binding / Interferon alpha/beta signaling / viral capsid / PIP3 activates AKT signaling / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / 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 (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Coronavirus nucleocapsid
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodSOLID-STATE NMR / simulated annealing
AuthorsSarkar, S. / Runge, B. / Russell, R.W. / Calero, D. / Zeinalilathori, S. / Quinn, C.M. / Lu, M. / Calero, G. / Gronenborn, A.M. / Polenova, T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5P50AI150481 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5 P30 GM110758-02 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Atomic-Resolution Structure of SARS-CoV-2 Nucleocapsid Protein N-Terminal Domain.
Authors: Sarkar, S. / Runge, B. / Russell, R.W. / Movellan, K.T. / Calero, D. / Zeinalilathori, S. / Quinn, C.M. / Lu, M. / Calero, G. / Gronenborn, A.M. / Polenova, T.
History
DepositionSep 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 29, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 14, 2023Group: Advisory / Other / Category: pdbx_database_remark / pdbx_database_status
Item: _pdbx_database_remark.text / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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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)14,9951
Polymers14,9951
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 14994.733 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0DTC9

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D CORD 25 ms
121isotropic12D CORD 100 ms
131isotropic12D CORD 250 ms
141isotropic12D CORD 500 ms
151isotropic12D NCACX 25 ms
161isotropic12D NCOCX 25 ms
171isotropic12D CP RFDR
181isotropic12D hNH HETCOR
191isotropic12D hCH HETCOR
1101isotropic13D hCANH
1111isotropic13D hCONH

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Sample preparation

DetailsType: solid / Contents: 30 mg/mL [U-100% 13C; U-100% 15N] N-NTD, water / Label: SARS-CoV-2 N-NTD / Solvent system: water
SampleConc.: 30 mg/mL / Component: N-NTD / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 50 mM / Label: 100%[U-13C,U-15N]-N-NTD / pH: 6.2 / Pressure: 1 atm / Temperature: 298.15 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisStevens TJ, Fogh RH, Boucher W, Higman VA, Eisenmenger F, Bardiaux B, van Rossum BJ, Oschkinat H, Laue EDdata analysis
NMRFAM-SPARKYLee W, Tonelli M, Markley JLchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 10

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