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Yorodumi- EMDB-22371: Cryo-EM structure of RIG-I:dsRNA filament in complex with RIPLET ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22371 | |||||||||
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Title | Cryo-EM structure of RIG-I:dsRNA filament in complex with RIPLET PrySpry domain (trimer) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | 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 / positive regulation of interferon-alpha production / TRAF6 mediated NF-kB activation / protein K63-linked ubiquitination / 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 / RING-type E3 ubiquitin transferase / response to virus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / protein homooligomerization / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / positive regulation of interleukin-6 production / ruffle membrane / cytoplasmic stress granule / protein polyubiquitination / ubiquitin-protein transferase activity / positive regulation of tumor necrosis factor production / SARS-CoV-1 activates/modulates innate immune responses / 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 / GTP binding / positive regulation of gene expression / 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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Kato K / Ahmad S | |||||||||
Funding support | United States, 1 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22371.map.gz | 8.9 MB | EMDB map data format | |
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Header (meta data) | emd-22371-v30.xml emd-22371.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
Images | emd_22371.png | 220.4 KB | ||
Filedesc metadata | emd-22371.cif.gz | 6.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22371 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22371 | HTTPS FTP |
-Validation report
Summary document | emd_22371_validation.pdf.gz | 354.9 KB | Display | EMDB validaton report |
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Full document | emd_22371_full_validation.pdf.gz | 354.5 KB | Display | |
Data in XML | emd_22371_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | emd_22371_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22371 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22371 | HTTPS FTP |
-Related structure data
Related structure data | 7jl3MC 7jl0C 7jl1C 7jl2C 7jl4C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22371.map.gz / Format: CCP4 / Size: 115.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : Ternary complex of dsRNA-bound RIG-I filament with RIPLET PrySpry...
Entire | Name: Ternary complex of dsRNA-bound RIG-I filament with RIPLET PrySpry domain |
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Components |
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-Supramolecule #1: Ternary complex of dsRNA-bound RIG-I filament with RIPLET PrySpry...
Supramolecule | Name: Ternary complex of dsRNA-bound RIG-I filament with RIPLET PrySpry domain type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-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: 3 / Enantiomer: LEVO / EC number: RNA helicase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 82.72407 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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 #2: E3 ubiquitin-protein ligase RNF135
Macromolecule | Name: E3 ubiquitin-protein ligase RNF135 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 21.021904 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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 #3: dsRNA strand1
Macromolecule | Name: dsRNA strand1 / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.550107 KDa |
Sequence | String: GACUGACUGA CUGAGACUGA CUGACUGAGA CUGACUGACU GA |
-Macromolecule #4: dsRNA strand 2
Macromolecule | Name: dsRNA strand 2 / type: rna / ID: 4 / Number of copies: 1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.360916 KDa |
Sequence | String: UCAGUCAGUC AGUCUCAGUC AGUCAGUCUC AGUCAGUCAG UC |
-Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 3 / 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: 3 / 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: 3 / 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: 3 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 46.2706 Å Applied symmetry - Helical parameters - Δ&Phi: 76.1005 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39718 |
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Startup model | Type of model: OTHER / Details: Featureless cylinder |
Final angle assignment | Type: NOT APPLICABLE |