SASDBM8: Probable ATP-dependent RNA helicase DDX58 (Delta-CARDs RIG-I) plu...

Basic information

• Entry: Database: SASBDB / ID: SASDBM8

Sample

Probable ATP-dependent RNA helicase DDX58 (Delta-CARDs RIG-I) plus 8mer hairpin dsRNA (SEC-peak1)

• Probable ATP-dependent RNA helicase DDX58 (without CARDs) (protein), DC-RIG-I, Homo sapiens
• 5´ppp 8mer hairpin dsRNA (RNA), 8bp

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 / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of granulocyte macrophage colony-stimulating factor production / cellular response to exogenous dsRNA / pattern recognition receptor activity / TRAF6 mediated IRF7 activation / 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 / 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

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 #946: ; Type: other / Software: (v2.1) / Symmetry: p1 / Chi-square value: 0.407; Search similar-shape structures of this assembly by Omokage search (details)
• Model #947: ; Type: other / Software: (v2.1) / Symmetry: p1 / Chi-square value: 0.407; Search similar-shape structures of this assembly by Omokage search (details)
• Model #948: ; Type: other / Software: (v2.1) / Symmetry: p1 / Chi-square value: 0.407; Search similar-shape structures of this assembly by Omokage search (details)
• Model #949: ; Type: dummy / Software: (v1.1.2) / Radius of dummy atoms: 3.25 A / Symmetry: p1 / Chi-square value: 0.426; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Probable ATP-dependent RNA helicase DDX58 (Delta-CARDs RIG-I) plus 8mer hairpin dsRNA (SEC-peak1); Entity id: 547 / 550
• Buffer: Name: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT; pH: 7.4

Entity #547

Name: DC-RIG-I / Type: protein
Description: Probable ATP-dependent RNA helicase DDX58 (without CARDs)
Formula weight: 79.77 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: O95786
Sequence:

MHHHHHHAAA SPFKPRNYQL ELALPAMKGK NTIICAPTGC GKTFVSLLIC EHHLKKFPQG QKGKVVFFAN QIPVYEQQKS VFSKYFERHG YRVTGISGAT AENVPVEQIV ENNDIIILTP QILVNNLKKG TIPSLSIFTL MIFDECHNTS KQHPYNMIMF NYLDQKLGGS SGPLPQVIGL TASVGVGDAK NTDEALDYIC KLCASLDASV IATVKHNLEE LEQVVYKPQK FFRKVESRIS DKFKYIIAQL MRDTESLAKR ICKDLENLSQ IQNREFGTQK YEQWIVTVQK ACMVFQMPDK DEESRICKAL FLYTSHLRKY NDALIISEHA RMKDALDYLK DFFSNVRAAG FDEIEQDLTQ RFEEKLQELE SVSRDPSNEN PKLEDLCFIL QEEYHLNPET ITILFVKTRA LVDALKNWIE GNPKLSFLKP GILTGRGKTN QNTGMTLPAQ KCILDAFKAS GDHNILIATS VADEGIDIAQ CNLVILYEYV GNVIKMIQTR GRGRARGSKC FLLTSNAGVI EKEQINMYKE KMMNDSILRL QTWDEAVFRE KILHIQTHEK FIRDSQEKPK PVPDKENKKL LCRKCKALAC YTADVRVIEE CHYTVLGDAF KECFVSRPHP KPKQFSSFEK RAKIFCARQN CSHDWGIHVK YKTFEIPVIK IESFVVEDIA TGVQTLYSKW KDFHFEKIPF DPAEMSK

Entity #550

Name: 8bp / Type: RNA / Description: 5´ppp 8mer hairpin dsRNA / Formula weight: 6.484 / Num. of mol.: 1
Sequence:

GGCGCGGCUU CGGCCGCGCC

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: Delta-CARDs RIG-I, 8mer hairpin dsRNA, SEC-peak1 / Measurement date: May 29, 2015 / Storage temperature: 4 °C / Cell temperature: 15 °C / Exposure time: 2 sec. / Number of frames: 17 / Unit: 1/A /

	Min	Max
Q	0.0174	0.2492

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 468 /

	Min	Max
Q	0.0174068	0.2
P(R) point	1	468
R	0	115.8

Result

Type of curve: merged /

	Experimental	Porod
MW	86.3 kDa	77.5 kDa
Volume	-	131.8 nm3

	P(R)	Guinier
Forward scattering, I0	0.0161	0.0162
Radius of gyration, Rg	3.43 nm	3.37 nm

	Min	Max
D	-	11.58
Guinier point	26	80