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- PDB-8th5: Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8th5 | ||||||
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Title | Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2 nucleocapsid protein P13L mutant | ||||||
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![]() | Hydrolase/Viral Protein / NTF2L USP10 / PEPTIDE BINDING PROTEIN / Hydrolase-Viral Protein complex | ||||||
Function / homology | ![]() DNA/RNA helicase activity / positive regulation of stress granule assembly / 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 ...DNA/RNA helicase activity / positive regulation of stress granule assembly / 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 / ribosomal small subunit binding / positive regulation of type I interferon production / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / stress granule assembly / DNA helicase activity / 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 / negative regulation of canonical Wnt signaling pathway / MHC class I protein complex / cytoplasmic stress granule / 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 / perikaryon / endonuclease activity / defense response to virus / Translation of Structural Proteins / Virion Assembly and Release / DNA helicase / host extracellular space / Induction of Cell-Cell Fusion / Ras protein signal transduction / Attachment and Entry / RNA helicase activity / host cell perinuclear region of cytoplasm / RNA helicase / ribonucleoprotein complex / innate immune response / focal adhesion / mRNA binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / ATP hydrolysis activity / DNA binding / RNA binding / extracellular region / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hughes, M.P. / Taylor, J.P. / Yang, Z. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Interaction between host G3BP and viral nucleocapsid protein regulates SARS-CoV-2 replication and pathogenicity. Authors: Yang, Z. / Johnson, B.A. / Meliopoulos, V.A. / Ju, X. / Zhang, P. / Hughes, M.P. / Wu, J. / Koreski, K.P. / Clary, J.E. / Chang, T.C. / Wu, G. / Hixon, J. / Duffner, J. / Wong, K. / Lemieux, ...Authors: Yang, Z. / Johnson, B.A. / Meliopoulos, V.A. / Ju, X. / Zhang, P. / Hughes, M.P. / Wu, J. / Koreski, K.P. / Clary, J.E. / Chang, T.C. / Wu, G. / Hixon, J. / Duffner, J. / Wong, K. / Lemieux, R. / Lokugamage, K.G. / Alvarado, R.E. / Crocquet-Valdes, P.A. / Walker, D.H. / Plante, K.S. / Plante, J.A. / Weaver, S.C. / Kim, H.J. / Meyers, R. / Schultz-Cherry, S. / Ding, Q. / Menachery, V.D. / Taylor, J.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 264.8 KB | Display | ![]() |
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PDB format | ![]() | 213.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 540.6 KB | Display | ![]() |
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Full document | ![]() | 563.7 KB | Display | |
Data in XML | ![]() | 45.6 KB | Display | |
Data in CIF | ![]() | 62.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8th1C ![]() 8th6C ![]() 8th7C 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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5 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15899.076 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 2622.785 Da / Num. of mol.: 7 / Mutation: P13L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.01 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M lithium sulfate, 0.1 M Tris pH 8.5, 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→92.77 Å / Num. obs: 31252 / % possible obs: 71.4 % / Redundancy: 3.5 % / CC1/2: 0.898 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.62→2.74 Å / Rmerge(I) obs: 0.37 / Num. unique obs: 440 / % possible all: 7.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 mean: 34.173 Å2
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Refinement step | Cycle: 1 / Resolution: 2.62→46.7 Å
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Refine LS restraints |
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