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- SASDBB8: Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) plu... -
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Open data
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Basic information
Entry | Database: SASBDB / ID: SASDBB8 |
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![]() | Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) plus 10mer hairpin dsRNA and ADP-AlFx
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Function / homology | ![]() 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 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 / cellular response to exogenous dsRNA / response to exogenous dsRNA / TRAF6 mediated NF-kB activation / positive regulation of interferon-alpha production / bicellular tight junction / 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 / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to virus / Evasion by RSV of host interferon responses / ISG15 antiviral mechanism / ruffle membrane / positive regulation of interleukin-6 production / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of tumor necrosis factor production / 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 / 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 / cytosol / cytoplasm Similarity search - Function |
Biological species | ![]() |
![]() | ![]() Title: Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis. Authors: Neelam Shah / Simone A Beckham / Jacqueline A Wilce / Matthew C J Wilce / ![]() Abstract: RIG-I (retinoic acid inducible gene-I) is a cytosolic innate immune protein that senses viral dsRNA with a 5'-triphosphate overhang. Upon interaction with dsRNA a de-repression of the RIG-I CARD ...RIG-I (retinoic acid inducible gene-I) is a cytosolic innate immune protein that senses viral dsRNA with a 5'-triphosphate overhang. Upon interaction with dsRNA a de-repression of the RIG-I CARD domains takes place that ultimately leads to the production of type I interferons and pro-inflammatory cytokines. Here we investigate the RIG-I conformational rearrangement upon interaction with an activating 5'-triphosphate-10-base pair dsRNA hairpin loop (10bp) compared with a less active 5'-triphosphate-8-base pair dsRNA hairpin loop (8bp). We use size-exclusion chromatography-coupled small-angle X-ray scattering (SAXS) and limited tryptic digest experiments to show that that upon binding to 10 bp, but not 8 bp, RIG-I becomes extended and shows greater flexibility, reflecting the release of its CARDs. We also examined the effect of different ATP analogues on the conformational changes of RIG-I/dsRNA complexes. Of the analogues tested, the addition of ATP transition state analogue ADP-AlFx further assisted in the complete activation of RIG-I in complex with 10bp and also to some extent RIG-I bound to 8bp. Together these data provide solution-based evidence for the molecular mechanism of innate immune signaling by RIG-I as stimulated by short hairpin RNA and ATP. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
-Data source
SASBDB page | ![]() |
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-Related structure data
Related structure data | C: citing same article ( |
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Similar structure data |
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External links
Related items in Molecule of the Month |
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-Models
Model #841 | ![]() Type: other / Software: (v2.1) / Symmetry: p1 / Chi-square value: 0.282 ![]() |
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Model #842 | ![]() Type: other / Software: (v2.1) / Symmetry: p1 / Chi-square value: 0.282 ![]() |
Model #843 | ![]() Type: other / Software: (v2.1) / Symmetry: p1 / Chi-square value: 0.282 ![]() |
Model #845 | ![]() Type: other / Software: (v2.1) / Symmetry: p1 / Chi-square value: 0.282 ![]() |
Model #846 | ![]() Type: other / Software: (v2.1) / Symmetry: p1 / Chi-square value: 0.282 ![]() |
Model #847 | ![]() Type: other / Software: (v2.1) / Symmetry: p1 / Chi-square value: 0.282 ![]() |
Model #848 | ![]() Type: other / Software: (v2.1) / Symmetry: p1 / Chi-square value: 0.282 ![]() |
Model #849 | ![]() Type: other / Software: (v2.1) / Symmetry: p1 / Chi-square value: 0.282 ![]() |
Model #850 | ![]() Type: other / Software: (v2.1) / Symmetry: p1 / Chi-square value: 0.282 ![]() |
Model #851 | ![]() Type: other / Software: (v2.1) / Symmetry: p1 / Chi-square value: 0.282 ![]() |
Model #852 | ![]() Type: other / Software: (v2.1) / Symmetry: p1 / Chi-square value: 0.282 ![]() |
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Sample
![]() | Name: Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) plus 10mer hairpin dsRNA and ADP-AlFx Entity id: 448 / 551 |
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Buffer | Name: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 2mM ADP-AlFx pH: 7.4 |
Entity #448 | Name: RIG-I / Type: protein / Description: Probable ATP-dependent RNA helicase DDX58 / Formula weight: 107.421 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: O95786 Sequence: MHHHHHHTTE QRRSLQAFQD YIRKTLDPTY ILSYMAPWFR EEEVQYIQAE KNNKGPMEAA TLFLKFLLEL QEEGWFRGFL DALDHAGYSG LYEAIESWDF KKIEKLEEYR LLLKRLQPEF KTRIIPTDII SDLSECLINQ ECEEILQICS TKGMMAGAEK LVECLLRSDK ...Sequence: MHHHHHHTTE QRRSLQAFQD YIRKTLDPTY ILSYMAPWFR EEEVQYIQAE KNNKGPMEAA TLFLKFLLEL QEEGWFRGFL DALDHAGYSG LYEAIESWDF KKIEKLEEYR LLLKRLQPEF KTRIIPTDII SDLSECLINQ ECEEILQICS TKGMMAGAEK LVECLLRSDK ENWPKTLKLA LEKERNKFSE LWIVEKGIKD VETEDLEDKM ETSDIQIFYQ EDPECQNLSE NSCPPSEVSD TNLYSPFKPR NYQLELALPA MKGKNTIICA PTGCGKTFVS LLICEHHLKK FPQGQKGKVV FFANQIPVYE QQKSVFSKYF ERHGYRVTGI SGATAENVPV EQIVENNDII ILTPQILVNN LKKGTIPSLS IFTLMIFDEC HNTSKQHPYN MIMFNYLDQK LGGSSGPLPQ VIGLTASVGV GDAKNTDEAL DYICKLCASL DASVIATVKH NLEELEQVVY KPQKFFRKVE SRISDKFKYI IAQLMRDTES LAKRICKDLE NLSQIQNREF GTQKYEQWIV TVQKACMVFQ MPDKDEESRI CKALFLYTSH LRKYNDALII SEHARMKDAL DYLKDFFSNV RAAGFDEIEQ DLTQRFEEKL QELESVSRDP SNENPKLEDL CFILQEEYHL NPETITILFV KTRALVDALK NWIEGNPKLS FLKPGILTGR GKTNQNTGMT LPAQKCILDA FKASGDHNIL IATSVADEGI DIAQCNLVIL YEYVGNVIKM IQTRGRGRAR GSKCFLLTSN AGVIEKEQIN MYKEKMMNDS ILRLQTWDEA VFREKILHIQ THEKFIRDSQ EKPKPVPDKE NKKLLCRKCK ALACYTADVR VIEECHYTVL GDAFKECFVS RPHPKPKQFS SFEKRAKIFC ARQNCSHDWG IHVKYKTFEI PVIKIESFVV EDIATGVQTL YSKWKDFHFE KIPFDPAEMS K |
Entity #551 | Name: 10bp / Type: RNA / Description: 5´ppp 10mer hairpin dsRNA / Formula weight: 7.725 / Num. of mol.: 1 Sequence: GGACGUACGU UUCGACGUAC GUCC |
-Experimental information
Beam | Instrument name: Australian Synchrotron SAXS/WAXS / City: Melbourne / 国: Australia ![]() | |||||||||||||||||||||||||||
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Detector | Name: Pilatus 1M | |||||||||||||||||||||||||||
Scan |
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Distance distribution function P(R) |
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Result |
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