+Open data
-Basic information
Entry | Database: PDB / ID: 1bf5 | ||||||
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Title | TYROSINE PHOSPHORYLATED STAT-1/DNA COMPLEX | ||||||
Components |
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Keywords | GENE REGULATION/DNA / COMPLEX (SH2 DOMAIN-DNA) / SH2 DOMAIN / TRANSCRIPTION FACTOR / GENE REGULATION-DNA COMPLEX | ||||||
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 / macrophage derived foam cell differentiation ...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 / macrophage derived foam cell differentiation / 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-27 signaling / Interleukin-35 Signalling / positive regulation of mesenchymal cell proliferation / NOTCH3 Intracellular Domain Regulates Transcription / histone acetyltransferase binding / Interleukin-20 family signaling / type I interferon-mediated signaling pathway / Interleukin-6 signaling / response to type II interferon / positive regulation of nitric-oxide synthase biosynthetic process / ubiquitin-like protein ligase binding / negative regulation of endothelial cell proliferation / cell surface receptor signaling pathway via JAK-STAT / positive regulation of interferon-alpha production / cellular response to organic cyclic compound / Regulation of IFNA/IFNB signaling / cellular response to interferon-beta / RNA polymerase II core promoter sequence-specific DNA binding / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / negative regulation of angiogenesis / Regulation of IFNG signaling / type II interferon-mediated signaling pathway / response to nutrient / Growth hormone receptor signaling / response to mechanical stimulus / negative regulation of canonical NF-kappaB signal transduction / Signaling by CSF3 (G-CSF) / positive regulation of defense response to virus by host / tumor necrosis factor-mediated signaling pathway / response to cAMP / Downstream signal transduction / positive regulation of smooth muscle cell proliferation / 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 / nuclear receptor binding / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / response to hydrogen peroxide / PKR-mediated signaling / Signaling by SCF-KIT / Inactivation of CSF3 (G-CSF) signaling / cellular response to insulin stimulus / RNA polymerase II transcription regulator complex / ISG15 antiviral mechanism / cellular response to type II interferon / response to peptide hormone / transcription coactivator binding / defense response / Signaling by CSF1 (M-CSF) in myeloid cells / Regulation of RUNX2 expression and activity / Interferon gamma signaling / Interferon alpha/beta signaling / Signaling by ALK fusions and activated point mutants / double-stranded DNA binding / regulation of cell population proliferation / histone binding / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / defense response to virus / DNA-binding transcription factor activity, RNA polymerase II-specific / cadherin binding / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / axon / dendrite / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / nucleolus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.9 Å | ||||||
Authors | Kuriyan, J. / Zhao, Y. / Chen, X. / Vinkemeier, U. / Jeruzalmi, D. / Darnell Jr., J.E. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1998 Title: Crystal structure of a tyrosine phosphorylated STAT-1 dimer bound to DNA. Authors: Chen, X. / Vinkemeier, U. / Zhao, Y. / Jeruzalmi, D. / Darnell Jr., J.E. / Kuriyan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bf5.cif.gz | 140.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bf5.ent.gz | 109.8 KB | Display | PDB format |
PDBx/mmJSON format | 1bf5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bf5_validation.pdf.gz | 455.6 KB | Display | wwPDB validaton report |
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Full document | 1bf5_full_validation.pdf.gz | 505.4 KB | Display | |
Data in XML | 1bf5_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 1bf5_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/1bf5 ftp://data.pdbj.org/pub/pdb/validation_reports/bf/1bf5 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | A CRYSTALLOGRAPHIC 2-FOLD AXIS PASSES THROUGH THE CENTER OF THE DNA DUPLEX. THE ASYMMETRIC UNIT CONTAINS HALF OF THE DUPLEX, AND THUS THE OPERATION OF THE TWO-FOLD AXIS RESULTS IN A NET 1.0 OCCUPANCY WITHIN THE ASYMMETRIC UNIT. |
-Components
#1: DNA chain | Mass: 5475.567 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 |
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#2: DNA chain | Mass: 5555.615 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#3: Protein | Mass: 66657.312 Da / Num. of mol.: 1 / Fragment: RESIDUES 136-710 / Mutation: PHOSPHORYLATED TYR 701 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P42224 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.82 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 |
Detector | Detector: AREA DETECTOR / Date: Jan 2, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. obs: 23301 / % possible obs: 89.8 % / Observed criterion σ(I): 1 / Redundancy: 11.3 % / Rmerge(I) obs: 0.075 / Rsym value: 0.198 |
Reflection | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 30 Å / % possible obs: 89.8 % / Observed criterion σ(I): 1 / Num. measured all: 261200 |
Reflection shell | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 72.1 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 4.9 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.9→30 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 17.31 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→30 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 30 Å / σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 2.289 |