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- PDB-7ylb: Two monobodies recognizing the conserved epitopes of SARS-CoV-2 N... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ylb | ||||||
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Title | Two monobodies recognizing the conserved epitopes of SARS-CoV-2 N antigen applicable to the broad COVID-19 diagnosis | ||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / Engineered 10Fn3 / SARS-CoV-2 N / Monobody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Hu, M. / Du, Y. / Sun, R. / Hao, Q. | ||||||
Funding support | 1items
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![]() | ![]() Title: Two monobodies recognizing the conserved epitopes of SARS-CoV-2 N antigen applicable to the broad COVID-19 diagnosis Authors: Hu, M. / Du, Y. / Sun, R. / Hao, Q. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 246.8 KB | Display | ![]() |
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PDB format | ![]() | 198.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 533.8 KB | Display | ![]() |
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Full document | ![]() | 557.1 KB | Display | |
Data in XML | ![]() | 43.1 KB | Display | |
Data in CIF | ![]() | 59.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yldC ![]() 1fnaS ![]() 6yunS 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13562.218 Da / Num. of mol.: 8 / Fragment: CTD Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() #2: Protein | Mass: 10384.603 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-SO4 / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.5 % |
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Crystal grow | Temperature: 293.15 K / Method: evaporation / Details: 0.2M K2SO4, 18% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→138.261 Å / Num. obs: 74632 / % possible obs: 99.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.186 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.41→2.45 Å / Rmerge(I) obs: 0.945 / Num. unique obs: 3673 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6YUN, 1FNA Resolution: 2.41→138.261 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.821 / SU B: 12.799 / SU ML: 0.293 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.361 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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 | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 137.72 Å2 / Biso mean: 41.358 Å2 / Biso min: 15.18 Å2
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Refinement step | Cycle: final / Resolution: 2.41→138.261 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.41→2.468 Å / Rfactor Rfree error: 0
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