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Yorodumi- PDB-6yi3: The N-terminal RNA-binding domain of the SARS-CoV-2 nucleocapsid ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yi3 | ||||||
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Title | The N-terminal RNA-binding domain of the SARS-CoV-2 nucleocapsid phosphoprotein | ||||||
Components | Nucleoprotein | ||||||
Keywords | VIRAL PROTEIN / COVID-19 / RNA-binding domain / SARS / MERS | ||||||
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 / positive regulation of NLRP3 inflammasome complex assembly / intracellular non-membrane-bounded organelle / 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 / positive regulation of NLRP3 inflammasome complex assembly / intracellular non-membrane-bounded organelle / 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 | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | SOLUTION NMR / torsion angle dynamics / molecular dynamics | ||||||
Authors | Veverka, V. / Boura, E. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yi3.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6yi3.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 6yi3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/6yi3 ftp://data.pdbj.org/pub/pdb/validation_reports/yi/6yi3 | HTTPS FTP |
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-Related structure data
Related structure data | 7acsC 7actC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 1 mM [U-13C; U-15N] N-NTD, 25 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O Label: s1 / Solvent system: 95% H2O/5% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 125 mM / Label: c1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 850 MHz |
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-Processing
NMR software |
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Refinement |
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NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 40 |