+Open data
-Basic information
Entry | Database: PDB / ID: 5jek | ||||||
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Title | Phosphorylated MAVS in complex with IRF-3 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Innate Immunity / Signaling | ||||||
Function / homology | Function and homology information positive regulation of IP-10 production / regulation of peroxisome organization / RIG-I binding / IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / macrophage apoptotic process / positive regulation of chemokine (C-C motif) ligand 5 production / programmed necrotic cell death / positive regulation of myeloid dendritic cell cytokine production / CARD domain binding ...positive regulation of IP-10 production / regulation of peroxisome organization / RIG-I binding / IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / macrophage apoptotic process / positive regulation of chemokine (C-C motif) ligand 5 production / programmed necrotic cell death / positive regulation of myeloid dendritic cell cytokine production / CARD domain binding / TRIF-dependent toll-like receptor signaling pathway / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / protein localization to mitochondrion / positive regulation of response to cytokine stimulus / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / IRF3-mediated induction of type I IFN / positive regulation of type I interferon-mediated signaling pathway / peroxisomal membrane / mRNA transcription / toll-like receptor 4 signaling pathway / TRAF6 mediated IRF7 activation / negative regulation of type I interferon-mediated signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / DNA-binding transcription activator activity / immune system process / negative regulation of viral genome replication / type I interferon-mediated signaling pathway / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of interferon-alpha production / antiviral innate immune response / TRAF6 mediated NF-kB activation / positive regulation of type I interferon production / ubiquitin ligase complex / signaling adaptor activity / lipopolysaccharide-mediated signaling pathway / positive regulation of defense response to virus by host / TICAM1-dependent activation of IRF3/IRF7 / Regulation of innate immune responses to cytosolic DNA / activation of innate immune response / positive regulation of interferon-beta production / molecular condensate scaffold activity / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Negative regulators of DDX58/IFIH1 signaling / promoter-specific chromatin binding / positive regulation of interleukin-8 production / mitochondrial membrane / DDX58/IFIH1-mediated induction of interferon-alpha/beta / PKR-mediated signaling / ISG15 antiviral mechanism / cellular response to virus / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of protein import into nucleus / positive regulation of interleukin-6 production / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of DNA-binding transcription factor activity / Interferon gamma signaling / Interferon alpha/beta signaling / Ovarian tumor domain proteases / sequence-specific double-stranded DNA binding / positive regulation of tumor necrosis factor production / TRAF3-dependent IRF activation pathway / regulation of inflammatory response / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / mitochondrial outer membrane / sequence-specific DNA binding / molecular adaptor activity / DNA-binding transcription factor activity, RNA polymerase II-specific / defense response to bacterium / positive regulation of protein phosphorylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / innate immune response / apoptotic process / DNA damage response / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å | ||||||
Authors | Zhao, B. / Li, P. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Structural basis for concerted recruitment and activation of IRF-3 by innate immune adaptor proteins. Authors: Zhao, B. / Shu, C. / Gao, X. / Sankaran, B. / Du, F. / Shelton, C.L. / Herr, A.B. / Ji, J.Y. / Li, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jek.cif.gz | 208.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jek.ent.gz | 175.1 KB | Display | PDB format |
PDBx/mmJSON format | 5jek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/5jek ftp://data.pdbj.org/pub/pdb/validation_reports/je/5jek | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26901.416 Da / Num. of mol.: 2 / Fragment: UNP residues 189-427 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IRF3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14653 #2: Protein/peptide | Mass: 1880.922 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: SER-GLY-CYS-PHE-GLU-ASP-LEU-ALA-ILE-SEP-ALA-SER-THR-SER Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z434*PLUS #3: 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: 2.25 Å3/Da / Density % sol: 45.35 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris pH 5.5, 80 mM MgCl2, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 120 K |
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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: May 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→64 Å / Num. obs: 19995 / % possible obs: 100 % / Redundancy: 7.2 % / Net I/σ(I): 14.3 |
-Processing
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Refinement | Resolution: 2.4→63.661 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.33
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→63.661 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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