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Yorodumi- PDB-6zco: Crystal Structure of C-terminal Dimerization Domain of Nucleocaps... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zco | ||||||
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Title | Crystal Structure of C-terminal Dimerization Domain of Nucleocapsid Phosphoprotein from SARS-CoV-2, crystal form II | ||||||
Components | Nucleoprotein | ||||||
Keywords | VIRAL PROTEIN / Nucleoprotein / SARS Coronavirus 2 | ||||||
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 / viral capsid / PIP3 activates AKT signaling / Interferon alpha/beta 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: 1.361 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 | 6zco.cif.gz | 70 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zco.ent.gz | 50.4 KB | Display | PDB format |
PDBx/mmJSON format | 6zco.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zco_validation.pdf.gz | 412.4 KB | Display | wwPDB validaton report |
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Full document | 6zco_full_validation.pdf.gz | 412.5 KB | Display | |
Data in XML | 6zco_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 6zco_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/6zco ftp://data.pdbj.org/pub/pdb/validation_reports/zc/6zco | HTTPS FTP |
-Related structure data
Related structure data | 6yunSC 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.: 1 / Fragment: Dimerization domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Plasmid: PRSF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTC9 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.27 % |
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Crystal grow | Temperature: 277 K / Method: evaporation / Details: tba |
-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 6M / Detector: PIXEL / Date: Jun 5, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.36→44.096 Å / Num. obs: 34588 / % possible obs: 97.8 % / Redundancy: 7.6 % / Rpim(I) all: 0.016 / Rrim(I) all: 0.047 / Rsym value: 0.041 / Net I/av σ(I): 11.7 / Net I/σ(I): 20.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6yun Resolution: 1.361→30 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.968 / SU B: 3.352 / SU ML: 0.054 / SU R Cruickshank DPI: 0.0468 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.48 Å2 / Biso mean: 28.894 Å2 / Biso min: 14.85 Å2
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Refinement step | Cycle: final / Resolution: 1.361→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.362→1.397 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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