Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis.

Shah N, Beckham SA, Wilce JA, Wilce MCJ
Nucleic Acids Res 46(6):3169-3186 (2018 Apr 6)

PMID: 29346611 doi: 10.1093/nar/gkx1307

Submitted to SASBDB: 2016 Dec 11 Published in SASBDB: 2018 Jan 22

SASDB78 – Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) Sample: Probable ATP-dependent RNA helicase DDX58 monomer, 108 kDa Homo sapiens protein Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, pH: 7.4 Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2012 Apr 6 RgGuinier 4.3 nm Dmax 14.0 nm VolumePorod 186 nm3

SASDB88 – Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) plus ADP-AlFx Sample: Probable ATP-dependent RNA helicase DDX58 monomer, 108 kDa Homo sapiens protein Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 2mM ADP-AlFx, pH: 7.4 Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Nov 20 RgGuinier 4.2 nm Dmax 15.6 nm VolumePorod 190 nm3

SASDB98 – Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) plus bound 10mer hairpin dsRNA Sample: Probable ATP-dependent RNA helicase DDX58 monomer, 108 kDa Homo sapiens protein 5´ppp 10mer hairpin dsRNA monomer, 8 kDa RNA Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, pH: 7.4 Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 May 29 RgGuinier 4.1 nm Dmax 16.1 nm VolumePorod 160 nm3

SASDBA8 – Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) plus 10mer hairpin dsRNA /AMP-PNP Sample: Probable ATP-dependent RNA helicase DDX58 monomer, 108 kDa Homo sapiens protein 5´ppp 10mer hairpin dsRNA monomer, 8 kDa RNA Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 0.5 mM AMP-PNP, pH: 7.4 Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 May 28 RgGuinier 4.2 nm Dmax 17.0 nm VolumePorod 163 nm3

SASDBB8 – Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) plus 10mer hairpin dsRNA and ADP-AlFx Sample: Probable ATP-dependent RNA helicase DDX58 monomer, 108 kDa Homo sapiens protein 5´ppp 10mer hairpin dsRNA monomer, 8 kDa RNA Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 2mM ADP-AlFx, pH: 7.4 Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Nov 20 RgGuinier 4.0 nm Dmax 18.3 nm VolumePorod 156 nm3

SASDBD8 – Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) plus 8mer hairpin dsRNA (SEC-peak1) Sample: Probable ATP-dependent RNA helicase DDX58 monomer, 108 kDa Homo sapiens protein 5´ppp 8mer hairpin dsRNA monomer, 6 kDa RNA Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, pH: 7.4 Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Nov 20 RgGuinier 4.3 nm Dmax 15.3 nm VolumePorod 179 nm3

SASDBE8 – Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) 8mer hairpin dsRNA/AMP-PNP (SEC-peak1) Sample: Probable ATP-dependent RNA helicase DDX58 monomer, 108 kDa Homo sapiens protein 5´ppp 8mer hairpin dsRNA monomer, 6 kDa RNA Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 0.5 mM AMP-PNP, pH: 7.4 Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2016 Apr 27 RgGuinier 4.1 nm Dmax 15.0 nm VolumePorod 188 nm3

SASDBF8 – Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) 8mer hairpin dsRNA/ADP-AlFx (SECpeak1) Sample: Probable ATP-dependent RNA helicase DDX58 monomer, 108 kDa Homo sapiens protein 5´ppp 8mer hairpin dsRNA monomer, 6 kDa RNA Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 2mM ADP-AlFx, pH: 7.4 Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Nov 20 RgGuinier 4.2 nm Dmax 16.8 nm VolumePorod 178 nm3

SASDBG8 – Probable ATP-dependent RNA helicase DDX58 without CARDs (Delta-CARDs RIG-I) Sample: Probable ATP-dependent RNA helicase DDX58 (without CARDs) monomer, 80 kDa Homo sapiens protein Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, pH: 7.4 Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 May 29 RgGuinier 3.7 nm Dmax 13.0 nm VolumePorod 114 nm3

SASDBH8 – Probable ATP-dependent RNA helicase DDX58 without CARDs (Delta-CARDs RIG-I) plus ADP-AlFx Sample: Probable ATP-dependent RNA helicase DDX58 (without CARDs) monomer, 80 kDa Homo sapiens protein Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 2mM ADP-AlFx, pH: 7.4 Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Nov 20 RgGuinier 3.5 nm Dmax 14.0 nm VolumePorod 132 nm3

SASDBJ8 – Probable ATP-dependent RNA helicase DDX58 without CARDs (Delta-CARDs RIG-I) plus 10mer hairpin dsRNA Sample: Probable ATP-dependent RNA helicase DDX58 (without CARDs) monomer, 80 kDa Homo sapiens protein 5´ppp 10mer hairpin dsRNA monomer, 8 kDa RNA Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, pH: 7.4 Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 May 29 RgGuinier 2.8 nm Dmax 9.0 nm VolumePorod 146 nm3

SASDBK8 – Probable ATP-dependent RNA helicase DDX58 (Delta-CARDs RIG-I) plus 10mer hairpin dsRNA and AMP-PNP Sample: Probable ATP-dependent RNA helicase DDX58 (without CARDs) monomer, 80 kDa Homo sapiens protein 5´ppp 10mer hairpin dsRNA monomer, 8 kDa RNA Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 0.5 mM AMP-PNP, pH: 7.4 Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 May 29 RgGuinier 2.8 nm Dmax 9.0 nm VolumePorod 135 nm3

SASDBL8 – Probable ATP-dependent RNA helicase DDX58 (Delta-CARDs RIG-I) plus 10mer hairpin dsRNA and ADP-AlFx Sample: Probable ATP-dependent RNA helicase DDX58 (without CARDs) monomer, 80 kDa Homo sapiens protein 5´ppp 10mer hairpin dsRNA monomer, 8 kDa RNA Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 2mM ADP-AlFx, pH: 7.4 Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Nov 20 RgGuinier 2.8 nm Dmax 8.9 nm VolumePorod 137 nm3

SASDBM8 – Probable ATP-dependent RNA helicase DDX58 (Delta-CARDs RIG-I) plus 8mer hairpin dsRNA (SEC-peak1) Sample: Probable ATP-dependent RNA helicase DDX58 (without CARDs) monomer, 80 kDa Homo sapiens protein 5´ppp 8mer hairpin dsRNA monomer, 6 kDa RNA Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, pH: 7.4 Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 May 29 RgGuinier 3.4 nm Dmax 11.6 nm VolumePorod 132 nm3

SASDBN8 – Probable ATP-dependent RNA helicase DDX58 (Delta-CARDs) plus 8mer hairpin dsRNA/AMP-PNP (SEC-peak1) Sample: Probable ATP-dependent RNA helicase DDX58 (without CARDs) monomer, 80 kDa Homo sapiens protein 5´ppp 8mer hairpin dsRNA monomer, 6 kDa RNA Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 0.5 mM AMP-PNP, pH: 7.4 Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2016 Apr 27 RgGuinier 3.2 nm Dmax 11.1 nm VolumePorod 114 nm3

SASDBP8 – Probable ATP-dependent RNA helicase DDX58 (Delta-CARDs) plus 8mer hairpin dsRNA/ADP-AlFx (SEC-peak1) Sample: Probable ATP-dependent RNA helicase DDX58 (without CARDs) monomer, 80 kDa Homo sapiens protein 5´ppp 8mer hairpin dsRNA monomer, 6 kDa RNA Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 2mM ADP-AlFx, pH: 7.4 Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Nov 20 RgGuinier 3.0 nm Dmax 10.5 nm VolumePorod 132 nm3

SASDBQ8 – Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) plus 8mer hairpin dsRNA (SEC-peak2) Sample: Probable ATP-dependent RNA helicase DDX58 dimer, 215 kDa Homo sapiens protein 5´ppp 8mer hairpin dsRNA dimer, 13 kDa RNA Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, pH: 7.4 Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Nov 20 RgGuinier 5.7 nm Dmax 24.6 nm VolumePorod 389 nm3

SASDBR8 – Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I), 8mer hairpin dsRNA/AMP-PNP (SECpeak2) Sample: Probable ATP-dependent RNA helicase DDX58 dimer, 215 kDa Homo sapiens protein 5´ppp 8mer hairpin dsRNA dimer, 13 kDa RNA Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 0.5 mM AMP-PNP, pH: 7.4 Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2016 Apr 27 RgGuinier 5.8 nm Dmax 24.6 nm VolumePorod 450 nm3

SASDBS8 – Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) 8mer hairpin dsRNA/ADP-AlFx (SECpeak2) Sample: Probable ATP-dependent RNA helicase DDX58 dimer, 215 kDa Homo sapiens protein 5´ppp 8mer hairpin dsRNA dimer, 13 kDa RNA Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 2mM ADP-AlFx, pH: 7.4 Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Nov 20 RgGuinier 5.3 nm Dmax 25.1 nm VolumePorod 298 nm3

SASDBT8 – Probable ATP-dependent RNA helicase DDX58 (Delta-CARDs RIG-I) plus 8mer hairpin dsRNA (SEC-peak2) Sample: 5´ppp 8mer hairpin dsRNA dimer, 13 kDa RNA Probable ATP-dependent RNA helicase DDX58 (without CARDs) dimer, 160 kDa Homo sapiens protein Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, pH: 7.4 Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 May 29 RgGuinier 4.1 nm Dmax 15.0 nm VolumePorod 273 nm3

SASDBU8 – Probable ATP-dependent RNA helicase DDX58 (Delta-CARDs) plus 8mer hairpin dsRNA/AMP-PNP (SEC-peak2) Sample: 5´ppp 8mer hairpin dsRNA dimer, 13 kDa RNA Probable ATP-dependent RNA helicase DDX58 (without CARDs) dimer, 160 kDa Homo sapiens protein Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 0.5 mM AMP-PNP, pH: 7.4 Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2016 Apr 27 RgGuinier 3.8 nm Dmax 15.4 nm VolumePorod 226 nm3

SASDBV8 – Probable ATP-dependent RNA helicase DDX58 (Delta-CARDs) plus 8mer hairpin dsRNA/ADP-AlFx (SEC-peak2) Sample: 5´ppp 8mer hairpin dsRNA dimer, 13 kDa RNA Probable ATP-dependent RNA helicase DDX58 (without CARDs) dimer, 160 kDa Homo sapiens protein Buffer: 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 2mM ADP-AlFx, pH: 7.4 Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Nov 20 RgGuinier 3.9 nm Dmax 16.0 nm VolumePorod 230 nm3