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- PDB-2qfb: Crystal structure of the regulatory domain of human RIG-I with bo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2qfb | ||||||
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Title | Crystal structure of the regulatory domain of human RIG-I with bound Zn | ||||||
![]() | Probable ATP-dependent RNA helicase DDX58 | ||||||
![]() | HYDROLASE / Zinc finger / Alternative splicing / Antiviral defense / ATP-binding / Helicase / Immune response / Innate immunity / Interferon induction / Nucleotide-binding / Polymorphism / RNA-binding / Ubl conjugation | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cui, S. / Lammens, A. / Lammens, K. / Hopfner, K.P. | ||||||
![]() | ![]() Title: The C-Terminal Regulatory Domain Is the RNA 5'-Triphosphate Sensor of RIG-I. Authors: Cui, S. / Eisenacher, K. / Kirchhofer, A. / Brzozka, K. / Lammens, A. / Lammens, K. / Fujita, T. / Conzelmann, K.K. / Krug, A. / Hopfner, K.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 267.7 KB | Display | ![]() |
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PDB format | ![]() | 210.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2qfdSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | the biological assembly is a monomer |
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Components
#1: Protein | Mass: 16853.498 Da / Num. of mol.: 10 / Fragment: Regulatory domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O95786, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.27 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 10 Details: 0.1 M CHES, 18% w/v PEG 8000, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2006 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 40897 / Num. obs: 40897 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.54 % / Rsym value: 0.09 / Net I/σ(I): 8.97 |
Reflection shell | Resolution: 3→3.18 Å / Redundancy: 2.55 % / Mean I/σ(I) obs: 2.13 / Num. unique all: 5886 / Rsym value: 0.445 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2QFD Resolution: 3→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.18 Å / Num. reflection obs: 6606 |