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Yorodumi- PDB-7n0r: Structure of the SARS-CoV-2 N protein RNA-binding domain bound to... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7n0r | ||||||
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Title | Structure of the SARS-CoV-2 N protein RNA-binding domain bound to single-domain antibody C2 | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / nanobody / nucleocapsid / VIRUS / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
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 Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Ye, Q. / Corbett, K.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Front Immunol / Year: 2021 Title: Structural Basis for SARS-CoV-2 Nucleocapsid Protein Recognition by Single-Domain Antibodies. Authors: Ye, Q. / Lu, S. / Corbett, K.D. #1: Journal: Biorxiv / Year: 2021 Title: Structural basis for SARS-CoV-2 Nucleocapsid protein recognition by single-domain antibodies. Authors: Ye, Q. / Lu, 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 | 7n0r.cif.gz | 361.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n0r.ent.gz | 245.3 KB | Display | PDB format |
PDBx/mmJSON format | 7n0r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7n0r_validation.pdf.gz | 459.7 KB | Display | wwPDB validaton report |
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Full document | 7n0r_full_validation.pdf.gz | 461.8 KB | Display | |
Data in XML | 7n0r_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 7n0r_validation.cif.gz | 41.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/7n0r ftp://data.pdbj.org/pub/pdb/validation_reports/n0/7n0r | HTTPS FTP |
-Related structure data
Related structure data | 7n0iC 7r98C 7cdzS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/836 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14144.752 Da / Num. of mol.: 2 / Fragment: RNA-binding domain 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: Antibody | Mass: 14484.096 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.25 Å3/Da / Density % sol: 45.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris-HCl pH 8.5, 0.2 M LiSO4, and 20% PEG 4000 |
-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: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 11, 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: 1.42→77.12 Å / Num. obs: 95122 / % possible obs: 99.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 17.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.016 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 1.42→1.44 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 4475 / CC1/2: 0.976 / Rpim(I) all: 0.121 / % possible all: 94.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7CDZ Resolution: 1.42→52.49 Å / SU ML: 0.1302 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 15.1893 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: 22.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→52.49 Å
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Refine LS restraints |
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LS refinement shell |
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