+Open data
-Basic information
Entry | Database: PDB / ID: 5f98 | |||||||||
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Title | Crystal structure of RIG-I in complex with Cap-0 RNA | |||||||||
Components |
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Keywords | hydrolase/rna / Complex / RIG-I / capped RNA / self versus non-self / innate immunity / hydrolase-rna complex | |||||||||
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 / ruffle membrane / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to virus / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / 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 / double-stranded DNA binding / TRAF3-dependent IRF activation pathway / gene expression / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å | |||||||||
Authors | Wang, C. / Marcotrigiano, J. / Miller, M. / Jiang, F. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Structural basis for m7G recognition and 2'-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I. Authors: Devarkar, S.C. / Wang, C. / Miller, M.T. / Ramanathan, A. / Jiang, F. / Khan, A.G. / Patel, S.S. / Marcotrigiano, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f98.cif.gz | 828.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f98.ent.gz | 663.3 KB | Display | PDB format |
PDBx/mmJSON format | 5f98.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f98_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 5f98_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 5f98_validation.xml.gz | 131.4 KB | Display | |
Data in CIF | 5f98_validation.cif.gz | 178.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/5f98 ftp://data.pdbj.org/pub/pdb/validation_reports/f9/5f98 | HTTPS FTP |
-Related structure data
Related structure data | 5f9fC 5f9hC 5e3hS 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: 79594.734 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 #2: RNA chain | Mass: 7649.559 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: Cap-0 HP RNA (24-MER) / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-M7G / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 20% (w/v) PEG 3350, 0.2 M NaSCN, 100 mM MOPS (pH 7.8), 3.5% (v/v) 2,2,2-trifluoroethanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.116 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→84.003 Å / Num. obs: 92301 / % possible obs: 99.8 % / Redundancy: 14 % / Rmerge(I) obs: 0.56 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 3.3→3.4 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 1.9 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5E3H Resolution: 3.28→84.003 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.62 / 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: 3.28→84.003 Å
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Refine LS restraints |
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LS refinement shell |
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