+Open data
-Basic information
Entry | Database: PDB / ID: 7uw3 | ||||||
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Title | Structure of SARS-CoV-2 Nucleocapsid Protein N-Terminal Domain | ||||||
Components | Nucleoprotein | ||||||
Keywords | VIRAL PROTEIN / COVID-19 / Nucleoprotein / N-terminal domain | ||||||
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 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Calero, G. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2022 Title: Atomic-Resolution Structure of SARS-CoV-2 Nucleocapsid Protein N-Terminal Domain. Authors: Sarkar, S. / Runge, B. / Russell, R.W. / Movellan, K.T. / Calero, D. / Zeinalilathori, S. / Quinn, C.M. / Lu, M. / Calero, G. / Gronenborn, A.M. / Polenova, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uw3.cif.gz | 214.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uw3.ent.gz | 163.5 KB | Display | PDB format |
PDBx/mmJSON format | 7uw3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/7uw3 ftp://data.pdbj.org/pub/pdb/validation_reports/uw/7uw3 | HTTPS FTP |
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-Related structure data
Related structure data | 7sd4C 6m3mS S: Starting model for refinement C: citing same article (ref.) |
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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: 14994.733 Da / Num. of mol.: 4 / Fragment: N-terminal domain (UNP residues 40-174) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 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: 2.21 Å3/Da / Density % sol: 44.44 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 30% PEG4000, 100 mM MES, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 30, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→37.41 Å / Num. obs: 57729 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 32.95 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.039 / Rrim(I) all: 0.1 / Χ2: 0.81 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.7→1.73 Å / Num. unique obs: 3009 / CC1/2: 0.21 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6M3M Resolution: 1.7→37.41 Å / SU ML: 0.3598 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 41.5447 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: 54.71 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→37.41 Å
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Refine LS restraints |
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LS refinement shell |
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