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Yorodumi- PDB-6yun: 1.45 Angstrom Resolution Crystal Structure of C-terminal Dimeriza... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yun | ||||||
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Title | 1.45 Angstrom Resolution Crystal Structure of C-terminal Dimerization Domain of Nucleocapsid Phosphoprotein from SARS-CoV-2 | ||||||
Components | Nucleoprotein | ||||||
Keywords | VIRAL PROTEIN / SARS-CoV-2 COVID-19 Nucleocapsid Phosphoprotein | ||||||
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 | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å | ||||||
Authors | Zinzula, L. / Basquin, J. / Nagy, I. / Bracher, A. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2021 Title: High-resolution structure and biophysical characterization of the nucleocapsid phosphoprotein dimerization domain from the Covid-19 severe acute respiratory syndrome coronavirus 2. Authors: Zinzula, L. / Basquin, J. / Bohn, S. / Beck, F. / Klumpe, S. / Pfeifer, G. / Nagy, I. / Bracher, A. / Hartl, F.U. / Baumeister, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yun.cif.gz | 72.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yun.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 6yun.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/6yun ftp://data.pdbj.org/pub/pdb/validation_reports/yu/6yun | HTTPS FTP |
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-Related structure data
Related structure data | 6zcoC 2cjrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15122.770 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTC9 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7.8 / Details: 31% PEG 4K 0.2 M Lithium sulfate 50 mM Tris pH 7.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→46.86 Å / Num. obs: 411193 / % possible obs: 98.4 % / Redundancy: 8.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.034 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.44→1.52 Å / Num. unique obs: 44155 / CC1/2: 0.789 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CJR Resolution: 1.44→44.15 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.14 / Phase error: 17.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.44→44.15 Å
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Refine LS restraints |
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LS refinement shell |
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