+Open data
-Basic information
Entry | Database: PDB / ID: 7bah | ||||||
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Title | Structure of RIG-I CTD bound to OH-RNA | ||||||
Components |
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Keywords | IMMUNE SYSTEM / RNA recognition / innate immunity | ||||||
Function / homology | Function and homology information regulation of type III interferon production / RIG-I signaling pathway / positive regulation of myeloid dendritic cell cytokine production / OAS antiviral response / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / positive regulation of granulocyte macrophage colony-stimulating factor production / pattern recognition receptor activity / TRAF6 mediated IRF7 activation ...regulation of type III interferon production / RIG-I signaling pathway / positive regulation of myeloid dendritic cell cytokine production / OAS antiviral response / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / positive regulation of granulocyte macrophage colony-stimulating factor production / pattern recognition receptor activity / TRAF6 mediated IRF7 activation / cytoplasmic pattern recognition receptor signaling pathway / RSV-host interactions / cellular response to exogenous dsRNA / response to exogenous dsRNA / TRAF6 mediated NF-kB activation / positive regulation of interferon-alpha production / bicellular tight junction / antiviral innate immune response / positive regulation of defense response to virus by host / positive regulation of interferon-beta production / regulation of cell migration / positive regulation of interleukin-8 production / Negative regulators of DDX58/IFIH1 signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to virus / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / ruffle membrane / positive regulation of interleukin-6 production / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of tumor necrosis factor production / double-stranded RNA binding / Ovarian tumor domain proteases / actin cytoskeleton / TRAF3-dependent IRF activation pathway / gene expression / double-stranded DNA binding / defense response to virus / RNA helicase activity / single-stranded RNA binding / Ub-specific processing proteases / RNA helicase / ribonucleoprotein complex / innate immune response / ubiquitin protein ligase binding / positive regulation of gene expression / GTP binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Anand, K. / Hagelueken, G. / Fusshoeller, D. / Geyer, M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: A conserved isoleucine in the RNA sensor RIG-I controls immune tolerance to mitochondrial RNA Authors: de Regt, A.K. / Anand, K. / Gatterdam, K. / Hagelueken, G. / Hartmann, G. / Geyer, M. / Schlee, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bah.cif.gz | 175.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bah.ent.gz | 113.5 KB | Display | PDB format |
PDBx/mmJSON format | 7bah.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/7bah ftp://data.pdbj.org/pub/pdb/validation_reports/ba/7bah | HTTPS FTP |
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-Related structure data
Related structure data | 7baiC 3ncuS 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: 14810.255 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDX58 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O95786, RNA helicase #2: RNA chain | Mass: 3827.336 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.91 Å3/Da / Density % sol: 57.69 % |
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Crystal grow | Temperature: 283.15 K / Method: vapor diffusion / Details: 0.1 M Tris-HCl pH 8.0 0.2 M NaCl 18% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→43.92 Å / Num. obs: 33784 / % possible obs: 99.4 % / Redundancy: 10.9 % / Rrim(I) all: 0.117 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 10.9 % / Num. unique obs: 0 / Rrim(I) all: 0.81 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NCU Resolution: 1.89→43.92 Å / Cross valid method: FREE R-VALUE / σ(F): 18.66 / Phase error: 31.2474 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: 42.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→43.92 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 | Refine-ID: X-RAY DIFFRACTION
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