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Yorodumi- PDB-8d3f: Crystal structure of human STAT1 in complex with the repeat regio... -
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-Basic information
Entry | Database: PDB / ID: 8d3f | ||||||
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Title | Crystal structure of human STAT1 in complex with the repeat region from Toxoplasma protein TgIST | ||||||
Components | Signal transducer and activator of transcription 1-alpha/beta,Inhibitor of STAT1-dependent transcription TgIST | ||||||
Keywords | TRANSCRIPTION / Signal transduction / Transcriptional activation / Pathogen effector / Interferon signaling | ||||||
Function / homology | Function and homology information metanephric mesenchymal cell differentiation / negative regulation of metanephric nephron tubule epithelial cell differentiation / negative regulation by virus of viral protein levels in host cell / renal tubule development / ISGF3 complex / response to interferon-beta / metanephric mesenchymal cell proliferation involved in metanephros development / interleukin-27-mediated signaling pathway / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / CCR5 chemokine receptor binding ...metanephric mesenchymal cell differentiation / negative regulation of metanephric nephron tubule epithelial cell differentiation / negative regulation by virus of viral protein levels in host cell / renal tubule development / ISGF3 complex / response to interferon-beta / metanephric mesenchymal cell proliferation involved in metanephros development / interleukin-27-mediated signaling pathway / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / CCR5 chemokine receptor binding / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / tumor necrosis factor receptor binding / Signaling by cytosolic FGFR1 fusion mutants / blood circulation / Interleukin-35 Signalling / Interleukin-27 signaling / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of mesenchymal cell proliferation / histone acetyltransferase binding / macrophage derived foam cell differentiation / Interleukin-20 family signaling / Interleukin-6 signaling / type I interferon-mediated signaling pathway / response to type II interferon / ubiquitin-like protein ligase binding / positive regulation of nitric-oxide synthase biosynthetic process / negative regulation of endothelial cell proliferation / positive regulation of interferon-alpha production / cell surface receptor signaling pathway via JAK-STAT / cellular response to organic cyclic compound / Regulation of IFNA/IFNB signaling / RNA polymerase II core promoter sequence-specific DNA binding / cellular response to interferon-beta / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / type II interferon-mediated signaling pathway / Regulation of IFNG signaling / response to mechanical stimulus / negative regulation of canonical NF-kappaB signal transduction / Growth hormone receptor signaling / Signaling by CSF3 (G-CSF) / response to cAMP / positive regulation of defense response to virus by host / tumor necrosis factor-mediated signaling pathway / Downstream signal transduction / negative regulation of angiogenesis / response to nutrient / transcription corepressor binding / positive regulation of erythrocyte differentiation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / protein phosphatase 2A binding / response to cytokine / promoter-specific chromatin binding / nuclear receptor binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of smooth muscle cell proliferation / response to hydrogen peroxide / PKR-mediated signaling / defense response / Inactivation of CSF3 (G-CSF) signaling / Signaling by SCF-KIT / transcription coactivator binding / response to peptide hormone / ISG15 antiviral mechanism / cellular response to type II interferon / cellular response to insulin stimulus / RNA polymerase II transcription regulator complex / Regulation of RUNX2 expression and activity / Signaling by CSF1 (M-CSF) in myeloid cells / Interferon gamma signaling / Interferon alpha/beta signaling / regulation of cell population proliferation / histone binding / double-stranded DNA binding / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / defense response to virus / DNA-binding transcription factor activity, RNA polymerase II-specific / response to xenobiotic stimulus / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / axon / dendrite / chromatin / nucleolus / regulation of transcription by RNA polymerase II / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Toxoplasma gondii GT1 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å | ||||||
Authors | Huang, Z. / Liu, H. / Nix, J.C. / Amarasinghe, G.K. / Sibley, L.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: The intrinsically disordered protein TgIST from Toxoplasma gondii inhibits STAT1 signaling by blocking cofactor recruitment. Authors: Huang, Z. / Liu, H. / Nix, J. / Xu, R. / Knoverek, C.R. / Bowman, G.R. / Amarasinghe, G.K. / Sibley, L.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8d3f.cif.gz | 153.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8d3f.ent.gz | 95.1 KB | Display | PDB format |
PDBx/mmJSON format | 8d3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/8d3f ftp://data.pdbj.org/pub/pdb/validation_reports/d3/8d3f | HTTPS FTP |
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-Related structure data
Related structure data | 1bf5S S: Starting model for refinement |
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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: 73359.930 Da / Num. of mol.: 1 / Fragment: STAT1-binding region Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Toxoplasma gondii GT1 (eukaryote) Gene: STAT1, TGRH88_087790 / Production host: Escherichia coli (E. coli) / References: UniProt: P42224, UniProt: A0A7J6KA90 |
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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: 3.8 Å3/Da / Density % sol: 67.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-Tris pH 6.3-6.0, 3 M sodium chloride and 50 mM sodium citrate tribasic PH range: 6.0-6.3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0722 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Apr 18, 2021 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0722 Å / Relative weight: 1 |
Reflection | Resolution: 2.97→46.64 Å / Num. obs: 23640 / % possible obs: 100 % / Redundancy: 29 % / Biso Wilson estimate: 79.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.033 / Rrim(I) all: 0.179 / Rsym value: 0.176 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2.97→3.15 Å / Redundancy: 28.4 % / Rmerge(I) obs: 1.961 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3764 / CC1/2: 0.874 / Rpim(I) all: 0.372 / Rrim(I) all: 1.997 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BF5 Resolution: 2.97→46.64 Å / SU ML: 0.3952 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.8527 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 95.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.97→46.64 Å
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Refine LS restraints |
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LS refinement shell |
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