+Open data
-Basic information
Entry | Database: PDB / ID: 4fcj | ||||||
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Title | Crystal structure of the NTF2-like domain of human G3BP1 | ||||||
Components | Ras GTPase-activating protein-binding protein 1 | ||||||
Keywords | HYDROLASE / NTF2-like domain | ||||||
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 / endonuclease activity / defense response to virus / DNA helicase / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Vognsen, T. / Kristensen, O. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Crystal Structures of the Human G3BP1 NTF2-Like Domain Visualize FxFG Nup Repeat Specificity. Authors: Vognsen, T. / Moller, I.R. / Kristensen, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fcj.cif.gz | 125.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fcj.ent.gz | 97.5 KB | Display | PDB format |
PDBx/mmJSON format | 4fcj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fcj_validation.pdf.gz | 445.8 KB | Display | wwPDB validaton report |
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Full document | 4fcj_full_validation.pdf.gz | 448.5 KB | Display | |
Data in XML | 4fcj_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 4fcj_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/4fcj ftp://data.pdbj.org/pub/pdb/validation_reports/fc/4fcj | HTTPS FTP |
-Related structure data
Related structure data | 4fcmC 4iiaC 3q90S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16181.351 Da / Num. of mol.: 2 / Fragment: NTF2-like domain 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: Chemical | ChemComp-GOL / | #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: 2.07 Å3/Da / Density % sol: 40.54 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20% PEG3350, 0.1 M Bis-tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 9, 2011 |
Radiation | Monochromator: Bent Si (111) crystal, horizontally focusing. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→55.444 Å / Num. all: 34385 / Num. obs: 34326 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.62→1.66 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.632 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2447 / Rsym value: 0.632 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3Q90 Resolution: 1.62→28.135 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 20.98 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.548 Å2 / ksol: 0.375 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→28.135 Å
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Refine LS restraints |
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LS refinement shell |
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