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Yorodumi- PDB-6wzo: Structure of SARS-CoV-2 Nucleocapsid dimerization domain, P1 form -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wzo | ||||||
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Title | Structure of SARS-CoV-2 Nucleocapsid dimerization domain, P1 form | ||||||
Components | Nucleoprotein | ||||||
Keywords | VIRAL PROTEIN / SARS-CoV-2 / COVID-19 / nucleocapsid / RNA binding | ||||||
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 | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Ye, Q. / Corbett, K.D. | ||||||
Citation | Journal: Protein Sci. / Year: 2020 Title: Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein. Authors: Ye, Q. / West, A.M.V. / Silletti, S. / Corbett, K.D. #1: Journal: Biorxiv / Year: 2020 Title: Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein. Authors: Ye, Q. / West, A.M.V. / Silletti, S. / Corbett, K.D. #2: Journal: Protein Sci. / Year: 2020 Title: Architecture and self-assembly of the SARS-CoV-2 ucleocapsid protein Authors: Ye, Q. / West, A.M.V. / Silletti, S. / Corbett, K.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wzo.cif.gz | 326.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wzo.ent.gz | 222.2 KB | Display | PDB format |
PDBx/mmJSON format | 6wzo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wzo_validation.pdf.gz | 436.8 KB | Display | wwPDB validaton report |
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Full document | 6wzo_full_validation.pdf.gz | 437.2 KB | Display | |
Data in XML | 6wzo_validation.xml.gz | 24 KB | Display | |
Data in CIF | 6wzo_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/6wzo ftp://data.pdbj.org/pub/pdb/validation_reports/wz/6wzo | HTTPS FTP |
-Related structure data
Related structure data | 6wzqC 2gibS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/785 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13532.190 Da / Num. of mol.: 4 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: 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: 2.67 Å3/Da / Density % sol: 53.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM Sodium acetate pH 4.5, 50 mM Sodium/potassium tartrate, and 34% polyethylene glycol PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→66.43 Å / Num. obs: 96446 / % possible obs: 91.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 18 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.046 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.42→1.44 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3 / Num. unique obs: 3939 / CC1/2: 0.957 / Rrim(I) all: 0.363 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GIB Resolution: 1.42→66.43 Å / SU ML: 0.1297 / Cross valid method: FREE R-VALUE / σ(F): 1.16 / Phase error: 20.042 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→66.43 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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