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- PDB-7acs: The SARS-CoV-2 nucleocapsid phosphoprotein N-terminal domain in c... -

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Basic information

Entry
Database: PDB / ID: 7acs
TitleThe SARS-CoV-2 nucleocapsid phosphoprotein N-terminal domain in complex with 7mer dsRNA
Components
  • Nucleoprotein
  • RNA (5'-R(P*CP*AP*CP*UP*GP*AP*C)-3')
  • RNA (5'-R(P*GP*UP*CP*AP*GP*UP*G)-3')
KeywordsVIRAL PROTEIN / protein-RNA complex / docking
Function / homology
Function and homology information


cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / RNA stem-loop binding / Maturation of nucleoprotein / intracellular non-membrane-bounded organelle / positive regulation of NLRP3 inflammasome complex assembly / CD28 dependent PI3K/Akt signaling / MHC class I protein binding ...cytoplasmic capsid assembly / viral RNA genome packaging / response to host immune response / negative regulation of interferon-beta production / RNA stem-loop binding / Maturation of nucleoprotein / intracellular non-membrane-bounded organelle / positive regulation of NLRP3 inflammasome complex assembly / CD28 dependent PI3K/Akt signaling / MHC class I protein binding / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / molecular condensate scaffold activity / protein sequestering activity / VEGFR2 mediated vascular permeability / TAK1-dependent IKK and NF-kappa-B activation / DDX58/IFIH1-mediated induction of interferon-alpha/beta / NOD1/2 Signaling Pathway / MHC class I protein complex / Interleukin-1 signaling / viral capsid / Interferon alpha/beta signaling / 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, N-terminal / Coronavirus nucleocapsid / Nucleocapsid protein, C-terminal
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodSOLUTION NMR / molecular dynamics
AuthorsVeverka, V.
CitationJournal: Plos Pathog. / Year: 2020
Title: Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein.
Authors: Dinesh, D.C. / Chalupska, D. / Silhan, J. / Koutna, E. / Nencka, R. / Veverka, V. / Boura, E.
History
DepositionSep 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: 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
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
B: RNA (5'-R(P*CP*AP*CP*UP*GP*AP*C)-3')
C: RNA (5'-R(P*GP*UP*CP*AP*GP*UP*G)-3')


Theoretical massNumber of molelcules
Total (without water)19,5483
Polymers19,5483
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2110 Å2
ΔGint-15 kcal/mol
Surface area10930 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

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


Mass: 15129.853 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: RNA chain RNA (5'-R(P*CP*AP*CP*UP*GP*AP*C)-3')


Mass: 2180.371 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
#3: RNA chain RNA (5'-R(P*GP*UP*CP*AP*GP*UP*G)-3')


Mass: 2237.379 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: isotropic / Type: 2D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 100 uM [U-13C; U-15N] N-NTD, 100 uM RNA (5'-R(P*CP*AP*CP*UP*GP*AP*C)-3'), 100 uM RNA (5'-R(P*GP*UP*CP*AP*GP*UP*G)-3'), 20 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O
Label: s1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 uMN-NTD[U-13C; U-15N]1
100 uMRNA (5'-R(P*CP*AP*CP*UP*GP*AP*C)-3')natural abundance1
100 uMRNA (5'-R(P*GP*UP*CP*AP*GP*UP*G)-3')natural abundance1
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
Sample conditionsIonic strength: 70 mM / Label: c1 / pH: 5.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 850 MHz

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Processing

NMR softwareName: HADDOCK / Developer: Bonvin / Classification: structure calculation
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 30

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