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Yorodumi- PDB-6kyv: Crystal Structure of RIG-I and hairpin RNA with G-U wobble base pairs -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kyv | ||||||
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Title | Crystal Structure of RIG-I and hairpin RNA with G-U wobble base pairs | ||||||
Components |
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Keywords | IMMUNE SYSTEM / RIG-I / DDX58 / dsRNA / Wobble base pair | ||||||
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 / cellular response to exogenous dsRNA / 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 / bicellular tight junction / regulation of cell migration / positive regulation of defense response to virus by host / positive regulation of interferon-beta production / Negative regulators of DDX58/IFIH1 signaling / positive regulation of interleukin-8 production / response to virus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / ISG15 antiviral mechanism / ruffle membrane / positive regulation of interleukin-6 production / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of DNA-binding transcription factor activity / Ovarian tumor domain proteases / actin cytoskeleton / positive regulation of tumor necrosis factor production / double-stranded RNA binding / gene expression / TRAF3-dependent IRF activation pathway / 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 / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / 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: 3 Å | ||||||
Authors | Kim, K.-H. / Hwang, J. / Kim, J.H. / Son, K.-P. / Jang, Y. / Kim, M. / Kang, S.-J. / Lee, J.-O. / Choi, B.-S. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Rna Biol. / Year: 2020 Title: Structural and biophysical properties of RIG-I bound to dsRNA with G-U wobble base pairs. Authors: Kim, K.H. / Hwang, J. / Kim, J.H. / Son, K.P. / Jang, Y. / Kim, M. / Kang, S.J. / Lee, J.O. / Kang, J.Y. / Choi, B.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kyv.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6kyv.ent.gz | 692.5 KB | Display | PDB format |
PDBx/mmJSON format | 6kyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/6kyv ftp://data.pdbj.org/pub/pdb/validation_reports/ky/6kyv | HTTPS FTP |
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-Related structure data
Related structure data | 5f9fS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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6 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 7043.186 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Protein | Mass: 78308.250 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDX58 / Production host: Escherichia coli (E. coli) / References: UniProt: O95786, RNA helicase #3: Chemical | ChemComp-ZN / 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: 2.98 Å3/Da / Density % sol: 58.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15% PEG 3350 (w/v), 100mM MES pH 6.5, 100mM NaSCN, 20mM Na Citrate tribasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 3→36.565 Å / Num. obs: 116928 / % possible obs: 95.54 % / Redundancy: 6.3 % / Biso Wilson estimate: 64.05 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.07 / Rrim(I) all: 0.182 / Χ2: 3.117 / Net I/σ(I): 15.44 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 1.76 / Num. unique obs: 5596 / Rpim(I) all: 0.594 / Rrim(I) all: 1.526 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5F9F Resolution: 3→36.56 Å / SU ML: 0.3464 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.9583 / Stereochemistry target values: GeoStd + Monomer Library
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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: 62.68 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→36.56 Å
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Refine LS restraints |
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LS refinement shell |
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