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- PDB-7jl1: Cryo-EM structure of RIG-I:dsRNA in complex with RIPLET PrySpry d... -
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Basic information
Entry | Database: PDB / ID: 7jl1 | ||||||
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Title | Cryo-EM structure of RIG-I:dsRNA in complex with RIPLET PrySpry domain (monomer) | ||||||
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![]() | HYDROLASE/TRANSFERASE/RNA / Innate immunity / E3 ligase / helicase / antiviral signaling / RLR / dsRNA sensor / HYDROLASE-TRANSFERASE-RNA complex | ||||||
Function / homology | ![]() 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 / cytoplasmic pattern recognition receptor signaling pathway / RSV-host interactions / regulation of innate immune response / cellular response to exogenous dsRNA / response to exogenous dsRNA / TRAF6 mediated NF-kB activation / protein K63-linked ubiquitination / antiviral innate immune response / bicellular tight junction / positive regulation of interferon-alpha production / ribonucleoprotein complex binding / regulation of cell migration / positive regulation of defense response to virus by host / positive regulation of interferon-beta production / positive regulation of interleukin-8 production / Negative regulators of DDX58/IFIH1 signaling / RING-type E3 ubiquitin transferase / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to virus / protein homooligomerization / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / ruffle membrane / cytoplasmic stress granule / protein polyubiquitination / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / ubiquitin protein ligase activity / 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 / protein ubiquitination / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
![]() | Kato, K. / Ahmad, S. / Hur, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural analysis of RIG-I-like receptors reveals ancient rules of engagement between diverse RNA helicases and TRIM ubiquitin ligases. Authors: Kazuki Kato / Sadeem Ahmad / Zixiang Zhu / Janet M Young / Xin Mu / Sehoon Park / Harmit S Malik / Sun Hur / ![]() ![]() Abstract: RNA helicases and E3 ubiquitin ligases mediate many critical functions in cells, but their actions have largely been studied in distinct biological contexts. Here, we uncover evolutionarily conserved ...RNA helicases and E3 ubiquitin ligases mediate many critical functions in cells, but their actions have largely been studied in distinct biological contexts. Here, we uncover evolutionarily conserved rules of engagement between RNA helicases and tripartite motif (TRIM) E3 ligases that lead to their functional coordination in vertebrate innate immunity. Using cryoelectron microscopy and biochemistry, we show that RIG-I-like receptors (RLRs), viral RNA receptors with helicase domains, interact with their cognate TRIM/TRIM-like E3 ligases through similar epitopes in the helicase domains. Their interactions are avidity driven, restricting the actions of TRIM/TRIM-like proteins and consequent immune activation to RLR multimers. Mass spectrometry and phylogeny-guided biochemical analyses further reveal that similar rules of engagement may apply to diverse RNA helicases and TRIM/TRIM-like proteins. Our analyses suggest not only conserved substrates for TRIM proteins but also, unexpectedly, deep evolutionary connections between TRIM proteins and RNA helicases, linking ubiquitin and RNA biology throughout animal evolution. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 211.5 KB | Display | ![]() |
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PDB format | ![]() | 153.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 874.6 KB | Display | ![]() |
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Full document | ![]() | 882.2 KB | Display | |
Data in XML | ![]() | 27.7 KB | Display | |
Data in CIF | ![]() | 42.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 22369MC ![]() 7jl0C ![]() 7jl2C ![]() 7jl3C ![]() 7jl4C M: map data used to model this data 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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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 82724.070 Da / Num. of mol.: 1 / Fragment: UNP residues 159-880 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#4: Protein | Mass: 21021.904 Da / Num. of mol.: 1 / Fragment: RIPLET PrySpry domain (UNP residues 249-432) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8IUD6, RING-type E3 ubiquitin transferase |
-DsRNA strand ... , 2 types, 2 molecules XY
#2: RNA chain | Mass: 4486.731 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#3: RNA chain | Mass: 4423.667 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 4 types, 4 molecules ![](data/chem/img/ADP.gif)
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![](data/chem/img/MG.gif)
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#5: Chemical | ChemComp-ADP / |
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#6: Chemical | ChemComp-ALF / |
#7: Chemical | ChemComp-MG / |
#8: Chemical | ChemComp-ZN / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Ternary complex of RIG-I:dsRNA:RIPLET PrySpry / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 19.424 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.18rc6_3830: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74079 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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