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Yorodumi- PDB-8th7: Crystal Structure of the G3BP1 NTF2-like domain bound to the Capr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8th7 | ||||||
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Title | Crystal Structure of the G3BP1 NTF2-like domain bound to the Caprin1 peptide | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / NTF2L Caprin1 | ||||||
Function / homology | Function and homology information regulation of deadenylation-dependent decapping of nuclear-transcribed mRNA / DNA/RNA helicase activity / positive regulation of stress granule assembly / intracellular mRNA localization / positive regulation of dendritic spine morphogenesis / non-membrane-bounded organelle assembly / positive regulation of dendrite morphogenesis / intracellular non-membrane-bounded organelle / generation of neurons / cell leading edge ...regulation of deadenylation-dependent decapping of nuclear-transcribed mRNA / DNA/RNA helicase activity / positive regulation of stress granule assembly / intracellular mRNA localization / positive regulation of dendritic spine morphogenesis / non-membrane-bounded organelle assembly / positive regulation of dendrite morphogenesis / intracellular non-membrane-bounded organelle / generation of neurons / cell leading edge / ribosomal small subunit binding / positive regulation of type I interferon production / signaling adaptor activity / stress granule assembly / synapse assembly / DNA helicase activity / molecular condensate scaffold activity / molecular function activator activity / P-body / negative regulation of canonical Wnt signaling pathway / cytoplasmic stress granule / lamellipodium / Ras protein signal transduction / perikaryon / DNA helicase / endonuclease activity / defense response to virus / RNA helicase activity / negative regulation of translation / RNA helicase / ribonucleoprotein complex / innate immune response / focal adhesion / mRNA binding / synapse / dendrite / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / DNA binding / RNA binding / ATP binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å | ||||||
Authors | Hughes, M.P. / Taylor, J.P. / Yang, Z. | ||||||
Funding support | United States, 1items
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Citation | Journal: Cell Rep / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8th7.cif.gz | 74 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8th7.ent.gz | 54.2 KB | Display | PDB format |
PDBx/mmJSON format | 8th7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8th7_validation.pdf.gz | 446 KB | Display | wwPDB validaton report |
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Full document | 8th7_full_validation.pdf.gz | 451 KB | Display | |
Data in XML | 8th7_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 8th7_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/8th7 ftp://data.pdbj.org/pub/pdb/validation_reports/th/8th7 | HTTPS FTP |
-Related structure data
Related structure data | 8th1C 8th5C 8th6C 3q9oS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15986.153 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: G3BP1, G3BP / Production host: Escherichia coli (E. coli) / References: UniProt: Q13283, DNA helicase, RNA helicase #2: Protein/peptide | Mass: 2621.915 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CAPRIN1, GPIAP1, GPIP137, M11S1, RNG105 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14444 #3: 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: 1.99 Å3/Da / Density % sol: 38.08 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.8M tri-ammonium citrate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.18057 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.18057 Å / Relative weight: 1 |
Reflection | Resolution: 2.88→48.42 Å / Num. obs: 6159 / % possible obs: 99.5 % / Redundancy: 4.5 % / CC1/2: 0.938 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 2.88→2.955 Å / Num. unique obs: 966 / CC1/2: 0.837 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3Q9O Resolution: 2.88→48.41 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.87 / SU B: 23.778 / SU ML: 0.454 / Cross valid method: THROUGHOUT / ESU R Free: 0.512 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.789 Å2
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Refinement step | Cycle: 1 / Resolution: 2.88→48.41 Å
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