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Yorodumi- PDB-7vbd: Crystal structure of SARS-Cov-2 nucleocapsid N-terminal domain (N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vbd | ||||||
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Title | Crystal structure of SARS-Cov-2 nucleocapsid N-terminal domain (NTD) protein,pH8.0 | ||||||
Components | Nucleoprotein | ||||||
Keywords | VIRAL PROTEIN / SARS-Cov-2 / nucleocapsid | ||||||
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: 1.94 Å | ||||||
Authors | Zeng, P. / Zhou, X.L. / Zhong, F.L. / Li, J. / Zhang, J. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of SARS-Cov-2 nucleocapsid N-terminal domain (NTD) protein,pH8.0 Authors: Zeng, P. / Zhou, X.L. / Zhong, F.L. / Li, J. / Zhang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vbd.cif.gz | 129.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vbd.ent.gz | 80.6 KB | Display | PDB format |
PDBx/mmJSON format | 7vbd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vbd_validation.pdf.gz | 463.6 KB | Display | wwPDB validaton report |
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Full document | 7vbd_full_validation.pdf.gz | 467.4 KB | Display | |
Data in XML | 7vbd_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 7vbd_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/7vbd ftp://data.pdbj.org/pub/pdb/validation_reports/vb/7vbd | HTTPS FTP |
-Related structure data
Related structure data | 7cdzS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 13986.596 Da / Num. of mol.: 4 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Escherichia coli BL21 (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: 2.52 Å3/Da / Density % sol: 51.29 % Description: The entry contains friedel pairs in I_plus/minus columns |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: pH 8.0, 0.05M Tris,38% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→28.54 Å / Num. obs: 76395 / % possible obs: 99.3 % / Redundancy: 5.8 % / Biso Wilson estimate: 25.4161331912 Å2 / Rmerge(I) obs: 0.33 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.94→2.05 Å / Rmerge(I) obs: 0.483 / Num. unique obs: 38898 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7CDZ Resolution: 1.94→28.52 Å / SU ML: 0.280044095781 / Cross valid method: NONE / σ(F): 1.33598437877 / Phase error: 28.7824533846 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: The entry contains friedel pairs in I_plus/minus columns
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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: 30.0202524116 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→28.52 Å
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Refine LS restraints |
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LS refinement shell |
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