+Open data
-Basic information
Entry | Database: PDB / ID: 5jeo | ||||||
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Title | Phosphorylated Rotavirus NSP1 in complex with IRF-3 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Viral Immuinity | ||||||
Function / homology | Function and homology information IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / macrophage apoptotic process / host cytoskeleton / programmed necrotic cell death / TRIF-dependent toll-like receptor signaling pathway / IRF3-mediated induction of type I IFN / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / positive regulation of type I interferon-mediated signaling pathway ...IRF3 mediated activation of type 1 IFN / MDA-5 signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / macrophage apoptotic process / host cytoskeleton / programmed necrotic cell death / TRIF-dependent toll-like receptor signaling pathway / IRF3-mediated induction of type I IFN / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / positive regulation of type I interferon-mediated signaling pathway / mRNA transcription / toll-like receptor 4 signaling pathway / TRAF6 mediated IRF7 activation / DNA-binding transcription activator activity / immune system process / 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 / positive regulation of type I interferon production / lipopolysaccharide-mediated signaling pathway / TICAM1-dependent activation of IRF3/IRF7 / Regulation of innate immune responses to cytosolic DNA / positive regulation of interferon-beta production / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Negative regulators of DDX58/IFIH1 signaling / promoter-specific chromatin binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / ISG15 antiviral mechanism / cellular response to virus / DNA-binding transcription repressor activity, RNA polymerase II-specific / SARS-CoV-1 activates/modulates innate immune responses / Interferon gamma signaling / Interferon alpha/beta signaling / sequence-specific double-stranded DNA binding / TRAF3-dependent IRF activation pathway / regulation of inflammatory response / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / DNA-binding transcription activator activity, RNA polymerase II-specific / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / regulation of apoptotic process / host cell cytoplasm / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / apoptotic process / DNA damage response / chromatin / regulation of transcription by RNA polymerase II / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rotavirus A Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.719 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 | 5jeo.cif.gz | 115.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jeo.ent.gz | 94.2 KB | Display | PDB format |
PDBx/mmJSON format | 5jeo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/5jeo ftp://data.pdbj.org/pub/pdb/validation_reports/je/5jeo | 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 on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 2337.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rotavirus A / Production host: Escherichia coli (E. coli) / References: UniProt: Q99FX5*PLUS | ||
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#2: Protein | Mass: 26901.416 Da / Num. of mol.: 1 / 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 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES sodium pH7.5, 0.8 M NaH2PO4, 0.8 M KH2PO4 |
-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: Jul 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.719→44.893 Å / Num. obs: 42593 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / CC1/2: 0.823 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/av σ(I): 44.5 / Net I/σ(I): 44.5 |
Reflection shell | Resolution: 1.72→1.75 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 1.719→44.893 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.34 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.719→44.893 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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