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- PDB-7uxx: Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal domain -
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Open data
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Basic information
Entry | Database: PDB / ID: 7uxx | ||||||||||||
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Title | Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal domain | ||||||||||||
![]() | Nucleoprotein | ||||||||||||
![]() | RNA BINDING PROTEIN / Viral protein / SARS-CoV-2 / CTD / nucleocapsid | ||||||||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Bezerra, E.H.S. / Tonoli, C.C.C. / Soprano, A.S. / Franchini, K.G. / Trivella, D.B.B. / Benedetti, C.E. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery and structural characterization of chicoric acid as a SARS-CoV-2 nucleocapsid protein ligand and RNA binding disruptor. Authors: Mercaldi, G.F. / Bezerra, E.H.S. / Batista, F.A.H. / Tonoli, C.C.C. / Soprano, A.S. / Shimizu, J.F. / Nagai, A. / da Silva, J.C. / Filho, H.V.R. / do Nascimento Faria, J. / da Cunha, M.G. / ...Authors: Mercaldi, G.F. / Bezerra, E.H.S. / Batista, F.A.H. / Tonoli, C.C.C. / Soprano, A.S. / Shimizu, J.F. / Nagai, A. / da Silva, J.C. / Filho, H.V.R. / do Nascimento Faria, J. / da Cunha, M.G. / Zeri, A.C.M. / Nascimento, A.F.Z. / Proenca-Modena, J.L. / Bajgelman, M.C. / Rocco, S.A. / Lopes-de-Oliveira, P.S. / Cordeiro, A.T. / Bruder, M. / Marques, R.E. / Sforca, M.L. / Franchini, K.G. / Benedetti, C.E. / Figueira, A.C.M. / Trivella, D.B.B. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 170.8 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 37.1 KB | Display | |
Data in CIF | ![]() | 55.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7uxzC ![]() 7c22S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12813.391 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 100 mM Tris-HCl (pH 8.3), 30% PEG 4000, 0.2 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3236 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→43.81 Å / Num. obs: 58500 / % possible obs: 99.95 % / Redundancy: 2 % / CC1/2: 0.997 / Net I/σ(I): 9.33 |
Reflection shell | Resolution: 1.85→1.916 Å / Redundancy: 2 % / Num. unique obs: 5760 / CC1/2: 0.887 / % possible all: 99.98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7C22 Resolution: 1.85→43.81 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.143 / SU ML: 0.093 / Cross valid method: FREE R-VALUE / ESU R: 0.14 / ESU R Free: 0.131 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.406 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→43.81 Å
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Refine LS restraints |
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LS refinement shell |
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