+Open data
-Basic information
Entry | Database: PDB / ID: 7nuf | ||||||||||||
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Title | Vaccinia virus protein 018 in complex with STAT1 | ||||||||||||
Components |
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Keywords | TRANSCRIPTION / Transcription factor / Inhibitor / Complex / Viral | ||||||||||||
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 / macrophage derived foam cell differentiation / histone acetyltransferase binding / Interleukin-20 family signaling / type I interferon-mediated signaling pathway / Interleukin-6 signaling / response to type II interferon / ubiquitin-like protein ligase binding / positive regulation of nitric-oxide synthase biosynthetic process / negative regulation of endothelial cell proliferation / cell surface receptor signaling pathway via JAK-STAT / 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 / positive regulation of interferon-alpha production / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / Regulation of IFNG signaling / type II interferon-mediated signaling pathway / response to mechanical stimulus / Growth hormone receptor signaling / negative regulation of canonical NF-kappaB signal transduction / Signaling by CSF3 (G-CSF) / positive regulation of defense response to virus by host / response to cAMP / 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 / PKR-mediated signaling / response to hydrogen peroxide / Inactivation of CSF3 (G-CSF) signaling / Signaling by SCF-KIT / ISG15 antiviral mechanism / response to peptide hormone / defense response / transcription coactivator binding / cellular response to type II interferon / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / Regulation of RUNX2 expression and activity / Signaling by CSF1 (M-CSF) in myeloid cells / Interferon gamma signaling / Interferon alpha/beta signaling / Signaling by ALK fusions and activated point mutants / regulation of cell population proliferation / histone binding / double-stranded DNA binding / regulation of apoptotic process / Interleukin-4 and Interleukin-13 signaling / 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 / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Vaccinia virus | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.00040159011 Å | ||||||||||||
Authors | Pantelejevs, T. / Talbot-Cooper, C. / Smith, G.L. / Hyvonen, M. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Cell Host Microbe / Year: 2022 Title: Poxviruses and paramyxoviruses use a conserved mechanism of STAT1 antagonism to inhibit interferon signaling. Authors: Talbot-Cooper, C. / Pantelejevs, T. / Shannon, J.P. / Cherry, C.R. / Au, M.T. / Hyvonen, M. / Hickman, H.D. / Smith, G.L. #1: Journal: Biorxiv / Year: 2021 Title: A strategy to suppress STAT1 signalling conserved in pathogenic poxviruses and paramyxoviruses Authors: Talbot-Cooper, C. / Pantelejevs, T. / Shannon, J.P. / Cherry, C.R. / Au, M.T. / Hyvonen, M. / Hickman, H.D. / Smith, G.L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nuf.cif.gz | 278.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nuf.ent.gz | 199.3 KB | Display | PDB format |
PDBx/mmJSON format | 7nuf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nuf_validation.pdf.gz | 330 KB | Display | wwPDB validaton report |
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Full document | 7nuf_full_validation.pdf.gz | 331.6 KB | Display | |
Data in XML | 7nuf_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 7nuf_validation.cif.gz | 31.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/7nuf ftp://data.pdbj.org/pub/pdb/validation_reports/nu/7nuf | HTTPS FTP |
-Related structure data
Related structure data | 1yvlS 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: 63306.715 Da / Num. of mol.: 1 / Mutation: Delta183-190, H182A, E393A, E394A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STAT1 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: P42224 |
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#2: Protein/peptide | Mass: 2343.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vaccinia virus (strain Western Reserve) / References: UniProt: P17356 |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-ACE / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 300:300 nl drop of protein:condition Protein: 10 mg/ml STAT1:peptide complex in 20 mM Tris pH8.0, 300 mM NaCl, 1 mM EDTA, 5 mM TCEP Condition: 16% PEG 3350 (w/v), 175 mM KCl, 125 mM NH4SO4, |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2→80.42 Å / Num. obs: 44523 / % possible obs: 99.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 42.4700956008 Å2 / CC1/2: 1 / Rrim(I) all: 0.124 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2→2.04 Å / Redundancy: 4.3 % / Num. unique obs: 2186 / CC1/2: 0.4 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YVL Resolution: 2.00040159011→55.7514233699 Å / SU ML: 0.356742212896 / Cross valid method: FREE R-VALUE / σ(F): 1.3281749626 / Phase error: 33.2966966352 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: 61.7300126627 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.00040159011→55.7514233699 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -89.1890419879 Å / Origin y: -57.8580200028 Å / Origin z: 228.078960228 Å
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Refinement TLS group | Selection details: all |