+Open data
-Basic information
Entry | Database: PDB / ID: 7jfm | ||||||
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Title | Crystal structure of mouse phosphorylated IRF-3 bound to CBP | ||||||
Components |
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Keywords | IMMUNE SYSTEM / transcription factor / phosphorylation / innate immunity | ||||||
Function / homology | Function and homology information IRF3 mediated activation of type 1 IFN / TICAM1-dependent activation of IRF3/IRF7 / TRAF3-dependent IRF activation pathway / type I interferon production / IRF3-mediated induction of type I IFN / positive regulation of cytokine production => GO:0001819 / Negative regulators of DDX58/IFIH1 signaling / TRAF6 mediated IRF7 activation / Regulation of innate immune responses to cytosolic DNA / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) ...IRF3 mediated activation of type 1 IFN / TICAM1-dependent activation of IRF3/IRF7 / TRAF3-dependent IRF activation pathway / type I interferon production / IRF3-mediated induction of type I IFN / positive regulation of cytokine production => GO:0001819 / Negative regulators of DDX58/IFIH1 signaling / TRAF6 mediated IRF7 activation / Regulation of innate immune responses to cytosolic DNA / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / ISG15 antiviral mechanism / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / programmed necrotic cell death / TRIF-dependent toll-like receptor signaling pathway / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes / positive regulation of type I interferon-mediated signaling pathway / NFE2L2 regulating MDR associated enzymes / MRF binding / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / negative regulation of transcription by RNA polymerase I / NOTCH3 Intracellular Domain Regulates Transcription / NFE2L2 regulating anti-oxidant/detoxification enzymes / TRAF6 mediated IRF7 activation / peptide-lysine-N-acetyltransferase activity / FOXO-mediated transcription of cell death genes / NFE2L2 regulating tumorigenic genes / embryonic digit morphogenesis / immune system process / homeostatic process / type I interferon-mediated signaling pathway / protein acetylation / Notch-HLH transcription pathway / cellular response to exogenous dsRNA / response to exogenous dsRNA / Formation of paraxial mesoderm / positive regulation of transforming growth factor beta receptor signaling pathway / non-canonical NF-kappaB signal transduction / Zygotic genome activation (ZGA) / stimulatory C-type lectin receptor signaling pathway / acetyltransferase activity / positive regulation of interferon-alpha production / cellular response to nutrient levels / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / histone acetyltransferase complex / positive regulation of type I interferon production / Attenuation phase / regulation of cellular response to heat / histone acetyltransferase activity / lipopolysaccharide-mediated signaling pathway / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RORA activates gene expression / NPAS4 regulates expression of target genes / Regulation of lipid metabolism by PPARalpha / positive regulation of interferon-beta production / CD209 (DC-SIGN) signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to bacterium / Formation of the beta-catenin:TCF transactivating complex / Heme signaling / protein destabilization / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / NOTCH1 Intracellular Domain Regulates Transcription / chromatin DNA binding / Pre-NOTCH Transcription and Translation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / positive regulation of protein localization to nucleus / transcription corepressor activity / rhythmic process / cellular response to UV / Circadian Clock / sequence-specific double-stranded DNA binding / p53 binding / TRAF3-dependent IRF activation pathway / HATs acetylate histones / regulation of inflammatory response Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å | ||||||
Authors | Li, P. / Jing, T. / Zhao, B. | ||||||
Funding support | United States, 1items
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Citation | Journal: J Immunol. / Year: 2020 Title: The Structural Basis of IRF-3 Activation upon Phosphorylation. Authors: Jing, T. / Zhao, B. / Xu, P. / Gao, X. / Chi, L. / Han, H. / Sankaran, B. / Li, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jfm.cif.gz | 204.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jfm.ent.gz | 164.3 KB | Display | PDB format |
PDBx/mmJSON format | 7jfm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/7jfm ftp://data.pdbj.org/pub/pdb/validation_reports/jf/7jfm | HTTPS FTP |
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-Related structure data
Related structure data | 7jflC 5jemS 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: 23650.928 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Irf3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P70671 #2: Protein/peptide | Mass: 5274.103 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CREBBP, CBP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92793, histone acetyltransferase #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.53 Å3/Da / Density % sol: 51.46 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2 M ammonium citrate tribasic at pH 7.0, 12% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→51.44 Å / Num. obs: 28422 / % possible obs: 99.9 % / Redundancy: 12.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.027 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.23→2.3 Å / Num. unique obs: 2601 / CC1/2: 0.382 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JEM Resolution: 2.23→51.44 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.48 / Stereochemistry target values: ML
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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 max: 190.32 Å2 / Biso mean: 91.163 Å2 / Biso min: 45.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.23→51.44 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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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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