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- EMDB-22369: Cryo-EM structure of RIG-I:dsRNA in complex with RIPLET PrySpry d... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22369 | |||||||||
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Title | Cryo-EM structure of RIG-I:dsRNA in complex with RIPLET PrySpry domain (monomer) | |||||||||
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![]() | 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 | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
![]() | Kato K / Ahmad 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
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 11.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.5 KB 14.5 KB | Display Display | ![]() |
Images | ![]() | 132.5 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 422.7 KB | Display | ![]() |
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Full document | ![]() | 422.3 KB | Display | |
Data in XML | ![]() | 4.3 KB | Display | |
Data in CIF | ![]() | 4.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jl1MC ![]() 7jl0C ![]() 7jl2C ![]() 7jl3C ![]() 7jl4C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.04203 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Ternary complex of RIG-I:dsRNA:RIPLET PrySpry
Entire | Name: Ternary complex of RIG-I:dsRNA:RIPLET PrySpry |
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Components |
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-Supramolecule #1: Ternary complex of RIG-I:dsRNA:RIPLET PrySpry
Supramolecule | Name: Ternary complex of RIG-I:dsRNA:RIPLET PrySpry / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Antiviral innate immune response receptor RIG-I
Macromolecule | Name: Antiviral innate immune response receptor RIG-I / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 82.72407 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: METSDIQIFY QEDPECQNLS ENSCPPSEVS DTNLYSPFKP RNYQLELALP AMKGKNTIIC APTGCGKTFV SLLICEHHLK KFPQGQKGK VVFFANQIPV YEQQKSVFSK YFERHGYRVT GISGATAENV PVEQIVENND IIILTPQILV NNLKKGTIPS L SIFTLMIF ...String: METSDIQIFY QEDPECQNLS ENSCPPSEVS DTNLYSPFKP RNYQLELALP AMKGKNTIIC APTGCGKTFV SLLICEHHLK KFPQGQKGK VVFFANQIPV YEQQKSVFSK YFERHGYRVT GISGATAENV PVEQIVENND IIILTPQILV NNLKKGTIPS L SIFTLMIF DECHNTSKQH PYNMIMFNYL DQKLGGSSGP LPQVIGLTAS VGVGDAKNTD EALDYICKLC ASLDASVIAT VK HNLEELE QVVYKPQKFF RKVESRISDK FKYIIAQLMR DTESLAKRIC KDLENLSQIQ NREFGTQKYE QWIVTVQKAC MVF QMPDKD EESRICKALF LYTSHLRKYN DALIISEHAR MKDALDYLKD FFSNVRAAGF DEIEQDLTQR FEEKLQELES VSRD PSNEN PKLEDLCFIL QEEYHLNPET ITILFVKTRA LVDALKNWIE GNPKLSFLKP GILTGRGKTN QNTGMTLPAQ KCILD AFKA SGDHNILIAT SVADEGIDIA QCNLVILYEY VGNVIKMIQT RGRGRARGSK CFLLTSNAGV IEKEQINMYK EKMMND SIL RLQTWDEAVF REKILHIQTH EKFIRDSQEK PKPVPDKENK KLLCRKCKAL ACYTADVRVI EECHYTVLGD AFKECFV SR PHPKPKQFSS FEKRAKIFCA RQNCSHDWGI HVKYKTFEIP VIKIESFVVE DIATGVQTLY SKWKDFHFEK IPFDPAEM S K UniProtKB: Antiviral innate immune response receptor RIG-I |
-Macromolecule #4: E3 ubiquitin-protein ligase RNF135
Macromolecule | Name: E3 ubiquitin-protein ligase RNF135 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 21.021904 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: RRASRFAQWA IHPTFNLKSL SCSLEVSKDS RTVTVSHRPQ PYRWSCERFS TSQVLCSQAL SSGKHYWEVD TRNCSHWAVG VASWEMSRD QVLGRTMDSC CVEWKGTSQL SAWHMVKETV LGSDRPGVVG IWLNLEEGKL AFYSVDNQEK LLYECTISAS S PLYPAFWL YGLHPGNYLI IKQVKV UniProtKB: E3 ubiquitin-protein ligase RNF135 |
-Macromolecule #2: dsRNA strand 1
Macromolecule | Name: dsRNA strand 1 / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 4.486731 KDa |
Sequence | String: GACUGACUGA CUGA |
-Macromolecule #3: dsRNA strand 2
Macromolecule | Name: dsRNA strand 2 / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 4.423667 KDa |
Sequence | String: UCAGUCAGUC AGUC |
-Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Macromolecule #6: TETRAFLUOROALUMINATE ION
Macromolecule | Name: TETRAFLUOROALUMINATE ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: ALF |
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Molecular weight | Theoretical: 102.975 Da |
Chemical component information | ![]() ChemComp-ALF: |
-Macromolecule #7: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #8: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 19.424 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER / Details: Featureless cylinder |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74079 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |