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Yorodumi- PDB-7xhf: Crystal structure of the NTF2L domain of human G3BP1 in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xhf | ||||||
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Title | Crystal structure of the NTF2L domain of human G3BP1 in complex with the USP10 derived peptide | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / Complex / Stress granules / Lipid-lipid phase separation | ||||||
Function / homology | Function and homology information DNA/RNA helicase activity / positive regulation of stress granule assembly / ribosomal small subunit binding / positive regulation of type I interferon production / stress granule assembly / DNA helicase activity / molecular condensate scaffold activity / negative regulation of canonical Wnt signaling pathway / cytoplasmic stress granule / perikaryon ...DNA/RNA helicase activity / positive regulation of stress granule assembly / ribosomal small subunit binding / positive regulation of type I interferon production / stress granule assembly / DNA helicase activity / molecular condensate scaffold activity / negative regulation of canonical Wnt signaling pathway / cytoplasmic stress granule / perikaryon / DNA helicase / endonuclease activity / defense response to virus / Ras protein signal transduction / RNA helicase activity / RNA helicase / ribonucleoprotein complex / innate immune response / focal adhesion / mRNA binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / DNA binding / RNA binding / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å | ||||||
Authors | Dan, S. / Weimin, G. | ||||||
Funding support | China, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: Yin and yang regulation of stress granules by Caprin-1. Authors: Song, D. / Kuang, L. / Yang, L. / Wang, L. / Li, H. / Li, X. / Zhu, Z. / Shi, C. / Zhu, H. / Gong, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xhf.cif.gz | 68.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xhf.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 7xhf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/7xhf ftp://data.pdbj.org/pub/pdb/validation_reports/xh/7xhf | HTTPS FTP |
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-Related structure data
Related structure data | 7xhgC 4fcjS 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: 15899.076 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: 1951.051 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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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: 2.55 Å3/Da / Density % sol: 51.85 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.0; 19 % w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→70.9 Å / Num. obs: 9910 / % possible obs: 92.7 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.034 / Rrim(I) all: 0.099 / Net I/σ(I): 57.1 |
Reflection shell | Resolution: 2.68→2.73 Å / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 528 / CC1/2: 0.934 / Rpim(I) all: 0.187 / Rrim(I) all: 0.561 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4fcj Resolution: 2.68→70.9 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.922 / SU B: 12.211 / SU ML: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 3.549 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 129.3 Å2 / Biso mean: 54.434 Å2 / Biso min: 27.96 Å2
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Refinement step | Cycle: final / Resolution: 2.68→70.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.68→2.745 Å / Rfactor Rfree error: 0
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