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Yorodumi- PDB-4fcm: Crystal structure of the NTF2-like domain of human G3BP1 in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fcm | ||||||
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Title | Crystal structure of the NTF2-like domain of human G3BP1 in complex with a peptide | ||||||
Components |
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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: 2.69 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 | 4fcm.cif.gz | 126.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fcm.ent.gz | 99.4 KB | Display | PDB format |
PDBx/mmJSON format | 4fcm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fcm_validation.pdf.gz | 463.1 KB | Display | wwPDB validaton report |
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Full document | 4fcm_full_validation.pdf.gz | 465.8 KB | Display | |
Data in XML | 4fcm_validation.xml.gz | 13 KB | Display | |
Data in CIF | 4fcm_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/4fcm ftp://data.pdbj.org/pub/pdb/validation_reports/fc/4fcm | HTTPS FTP |
-Related structure data
Related structure data | 4fcjSC 4iiaC S: Starting model for refinement C: citing same article (ref.) |
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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: Protein/peptide | Mass: 931.967 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Chemical | ChemComp-PO4 / | #4: 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 Å3/Da / Density % sol: 38.48 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20% PEG3350, 0.1 M Bis-tris, pH 5.5, VAPOR DIFFUSION, SITTING 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: 2.69→28.38 Å / Num. all: 7987 / Num. obs: 7987 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 63.7 Å2 / Rmerge(I) obs: 0.129 / Rsym value: 0.15 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.69→2.76 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.943 / Mean I/σ(I) obs: 1.8 / Num. unique all: 566 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4fcj Resolution: 2.69→28.38 Å / SU ML: 0.55 / σ(F): 1.34 / Phase error: 28.96 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.93 Å2 / ksol: 0.357 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.69→28.38 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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