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Yorodumi- 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) | ||||||
Components |
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Keywords | HYDROLASE/TRANSFERASE/RNA / Innate immunity / E3 ligase / helicase / antiviral signaling / RLR / dsRNA sensor / HYDROLASE-TRANSFERASE-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 / 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 / positive regulation of interferon-alpha production / bicellular tight junction / ribonucleoprotein complex binding / 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 / RING-type E3 ubiquitin transferase / protein homooligomerization / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / cytoplasmic stress granule / positive regulation of interleukin-6 production / protein polyubiquitination / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / 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 / 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 / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Kato, K. / Ahmad, S. / Hur, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Mol Cell / Year: 2021 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7jl1.cif.gz | 211.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jl1.ent.gz | 153.4 KB | Display | PDB format |
PDBx/mmJSON format | 7jl1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jl1_validation.pdf.gz | 874.6 KB | Display | wwPDB validaton report |
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Full document | 7jl1_full_validation.pdf.gz | 882.2 KB | Display | |
Data in XML | 7jl1_validation.xml.gz | 27.7 KB | Display | |
Data in CIF | 7jl1_validation.cif.gz | 42.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/7jl1 ftp://data.pdbj.org/pub/pdb/validation_reports/jl/7jl1 | 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 (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: DDX58 / Production host: Escherichia coli (E. coli) / References: UniProt: O95786, RNA helicase |
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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.) Homo sapiens (human) / Gene: RNF135, L13 / Production host: Escherichia coli (E. coli) 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.) Homo sapiens (human) |
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#3: RNA chain | Mass: 4423.667 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-Non-polymers , 4 types, 4 molecules
#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 |
-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: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
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 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 19.424 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-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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