SASDB88: Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) pl...

Basic information

• Entry: Database: SASBDB / ID: SASDB88

Sample

Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) plus ADP-AlFx

• Probable ATP-dependent RNA helicase DDX58 (protein), RIG-I, Homo sapiens

Function / homology

Function:

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 / cellular response to exogenous dsRNA / RSV-host interactions / response to exogenous dsRNA / positive regulation of interferon-alpha production / TRAF6 mediated NF-kB activation / bicellular tight junction / positive regulation of defense response to virus by host / antiviral innate immune response / positive regulation of interferon-beta production / regulation of cell migration / positive regulation of interleukin-8 production / Negative regulators of DDX58/IFIH1 signaling / response to virus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / 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

Domain/homology:

RIG-I, CARD domain repeat 2 / RIG-I-like receptor, C-terminal / RIG-I receptor C-terminal domain / RIG-I-like receptor, C-terminal regulatory domain / RIG-I-like receptor, C-terminal domain superfamily / : / C-terminal domain of RIG-I / RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile. / Caspase recruitment domain / Caspase recruitment domain / Death-like domain superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase

Component:

Antiviral innate immune response receptor RIG-I

• Biological species: Homo sapiens (human)
• Citation: Journal: Nucleic Acids Res / Year: 2018; 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 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.

Contact author

• Neelam Shah (Monash University, Melbourne, Australia)

Models

• Model #858: ; Type: other / Software: (v2.1) / Symmetry: p1 / Chi-square value: 0.320; Search similar-shape structures of this assembly by Omokage search (details)
• Model #859: ; Type: other / Software: (v2.1) / Symmetry: p1 / Chi-square value: 0.320; Search similar-shape structures of this assembly by Omokage search (details)
• Model #860: ; Type: other / Software: (v2.1) / Symmetry: p1 / Chi-square value: 0.320; Search similar-shape structures of this assembly by Omokage search (details)
• Model #956: ; Type: dummy / Software: (v1.1.2) / Radius of dummy atoms: 3.75 A / Symmetry: p1 / Chi-square value: 0.289; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) plus ADP-AlFx
• 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 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

Experimental information

• Beam: Instrument name: Australian Synchrotron SAXS/WAXS / City: Melbourne / 国: Australia / Shape: Point / Type of source: X-ray synchrotron / Wavelength: 0.10332 Å / Dist. spec. to detc.: 1.6 mm
• Detector: Name: Pilatus 1M

Scan

Title: Full-length RIG-I with ADP-AlFx / Measurement date: Nov 20, 2015 / Storage temperature: 4 °C / Cell temperature: 15 °C / Exposure time: 2 sec. / Number of frames: 13 / Unit: 1/A /

	Min	Max
Q	0.0076	0.2506

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 347 /

	Min	Max
Q	0.00878155	0.143792
P(R) point	1	347
R	0	155.8

Result

Type of curve: merged /

	Experimental	Porod
MW	108.1 kDa	112 kDa
Volume	-	189.99 nm3

	P(R)	Guinier
Forward scattering, I0	0.0516	0.051
Radius of gyration, Rg	4.34 nm	4.19 nm

	Min	Max
D	-	15.6
Guinier point	6	58