+Open data
-Basic information
Entry | Database: PDB / ID: 8g7t | |||||||||
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Title | Cryo-EM structure of RNP end | |||||||||
Components |
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Keywords | Transferase/Hydrolase/RNA / ribonucleoprotein complex / RNA sensor / RIG-I like receptor / Ubiquitination / E3 ligase / TRIM family / ANTIVIRAL PROTEIN / Transferase-Hydrolase-RNA complex | |||||||||
Function / homology | Function and homology information RIG-I binding / free ubiquitin chain polymerization / 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 ...RIG-I binding / free ubiquitin chain polymerization / 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 innate immune response / cellular response to exogenous dsRNA / response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / protein K63-linked ubiquitination / positive regulation of interferon-alpha production / antiviral innate immune response / TRAF6 mediated NF-kB activation / bicellular tight junction / ribonucleoprotein complex binding / 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 / RING-type E3 ubiquitin transferase / DDX58/IFIH1-mediated induction of interferon-alpha/beta / protein homooligomerization / ISG15 antiviral mechanism / ruffle membrane / cytoplasmic stress granule / protein polyubiquitination / positive regulation of interleukin-6 production / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / 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 / protein ubiquitination / 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 / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Wang, W. / Pyle, A.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Cryo-EM structure of Riplet:RIG-I:dsRNA complex (end-inter) Authors: Wang, W. / Pyle, A.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8g7t.cif.gz | 341.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g7t.ent.gz | 259.1 KB | Display | PDB format |
PDBx/mmJSON format | 8g7t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/8g7t ftp://data.pdbj.org/pub/pdb/validation_reports/g7/8g7t | HTTPS FTP |
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-Related structure data
Related structure data | 29823MC 8g7uC 8g7vC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 106740.555 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 (E. coli) / References: UniProt: O95786, RNA helicase #2: Protein | Mass: 47946.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RNF135, L13 / Production host: Escherichia coli (E. coli) References: UniProt: Q8IUD6, RING-type E3 ubiquitin transferase #3: RNA chain | | Mass: 7885.581 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #4: RNA chain | | Mass: 7788.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #5: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex of RNP end / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 204993 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | B value: 76 / Space: REAL | ||||||||||||||||||||||||
Atomic model building |
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