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- SASDBA8: 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: SASDBA8 |
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![]() | Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) plus 10mer hairpin dsRNA /AMP-PNP
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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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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 #818 | ![]() Type: other / Software: (v2.1) / Symmetry ![]() ![]() |
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Model #819 | ![]() Type: other / Software: (v2.1) / Symmetry ![]() ![]() |
Model #820 | ![]() Type: other / Software: (v2.1) / Symmetry ![]() ![]() |
Model #821 | ![]() Type: other / Software: (v2.1) / Symmetry ![]() ![]() |
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Sample
![]() | Name: Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) plus 10mer hairpin dsRNA /AMP-PNP 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, 0.5 mM AMP-PNP pH: 7.4 |
Entity #448 | Name: RIG-I![]() 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 | |||||||||||||||||||||||||||
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Distance distribution function P(R) |
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Result |
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