SASDBG8

Probable ATP-dependent RNA helicase DDX58 without CARDs (Delta-CARDs RIG-I)

Data type: SASBDB experimental data Status: Published Curve type: Merged Last updated: 2019-12-06T13:07:15.624532+01:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Probable ATP-dependent RNA helicase DDX58 without CARDs (Delta-CARDs RIG-I)

Concentration— – — Buffer / pH25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT / 7.4
Experimental temperature15.0 Facility / beamlineAustralian Synchrotron / SAXS/WAXS
Wavelength0.10332 nmExposure2.0 s × 13

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Probable ATP-dependent RNA helicase DDX58 (without CARDs)
View sequence
MHHHHHHAAASPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQQKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVGVGDAKNTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKILHIQTHEKFIRDSQEKPKPVPDKENKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATGVQTLYSKWKDFHFEKIPFDPAEMSK
proteinHomo sapiensO95786239–925monomerMolecule count 179.77 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1595[3]0.0158421–0.250772 1/AHas uncertainty columnMissing 00sasbdb/entries/g8/sasdbg8/source/SASDBG8.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)12.98—Å
i0Guinier0.0348——
i0P(r)0.0348——
mwExperimental79.7—kDa
mwPorod68.5—kDa
porod_volumePorod113.99—ų
rgGuinier3.67—Å
rgP(r)3.78—Å

These values are reported by SASBDB; SAXSdb did not recalculate them from the experimental curve.

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3. Source Fits and Models Source Fits & Models

Fit 2 · DAMMIF v1.1.2

χ²: 0.478CorMap p: 0.979869Unit: 1/A
ModelName / TypeSoftwareSymmetryModel MWPDB DeclarationSource file
1—dummyDAMMIF v1.1.2p189.676—Model Image
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4. Source File Index Source Files

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5. Experiment Description and Publication Experiment & Publication

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6. Complete Source Record Complete Source Record

The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.

Open the original SASBDB entry

Buffer and Sample Properties

Buffer name25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTTBuffer concentration—
pH7.4Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2015-05-29Storage / measurement temperature4.0 / 15.0
Exposure time2.0Frames13
Wavelength0.10332Sample-to-detector distance1.6
SourceX-ray synchrotronDetectorPilatus 1M
Facility / beamlineAustralian Synchrotron / SAXS/WAXS · Melbourne, Australia
q range0.158 – 2.508Sample volume / flow rate— / —

Original SASBDB Plots

Experimental I(q)
Experimental I(q)
Experimental I(q), log-log
Experimental I(q), log-log
Guinier plot
Guinier plot
Kratky plot
Kratky plot
P(r) plot
P(r) plot

Downloadable Files

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full_entry_zip:source record and ZIP contents (6 items)
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pddf:source record
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sascif:source record
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All source fields (unfiltered)

Every source field is expanded here, including empty values, list members and fields already shown above.

summary.json:179 field values
Field pathRaw value
codeSASDBG8
statusPublished
type_of_curveMerged
angular_unit1/A
project.titleCombined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis.
project.publication.titleCombined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis.
project.publication.author_listShah N, Beckham SA, Wilce JA, Wilce MCJ
project.publication.journalNucleic Acids Res
project.publication.doi10.1093/nar/gkx1307
project.publication.pmid29346611
project.publication.published_date2018 Apr 6
project.statusreleased
project.submitted_date2016-12-11
project.released_date2018-01-22
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDBG8.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDBG8.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBG8_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBG8_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBG8_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBG8_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDBG8.sascif
experiment.instrument.detector.typeDectris
experiment.instrument.detector.namePilatus 1M
experiment.instrument.detector.resolution172.0
experiment.instrument.nameAustralian Synchrotron
experiment.instrument.cityMelbourne
experiment.instrument.countryAustralia
experiment.instrument.beamline_nameSAXS/WAXS
experiment.instrument.beam_geometryPoint
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourceTrue
experiment.instrument.line_collimationnull
experiment.instrument.sample_path_lengthnull
experiment.instrument.line_collimation_slitlengthnull
experiment.instrument.line_collimation_integrationwidthnull
experiment.instrument.xray_energynull
experiment.instrument.beam_profile_ahnull
experiment.instrument.beam_profile_alnull
experiment.sample.molecule[0].long_nameProbable ATP-dependent RNA helicase DDX58 (without CARDs)
experiment.sample.molecule[0].short_nameDC-RIG-I
experiment.sample.molecule[0].sequenceMHHHHHHAAASPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQQKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVGVGDAKNTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKILHIQTHEKFIRDSQEKPKPVPDKENKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATGVQTLYSKWKDFHFEKIPFDPAEMSK
experiment.sample.molecule[0].organismHomo sapiens
experiment.sample.molecule[0].uniprot_codeO95786
experiment.sample.molecule[0].uniprot_range_first239
experiment.sample.molecule[0].uniprot_range_last925
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMTTEQRRSLQAFQDYIRKTLDPTYILSYMAPWFREEEVQYIQAEKNNKGPMEAATLFLKF LLELQEEGWFRGFLDALDHAGYSGLYEAIESWDFKKIEKLEEYRLLLKRLQPEFKTRIIP TDIISDLSECLINQECEEILQICSTKGMMAGAEKLVECLLRSDKENWPKTLKLALEKERN KFSELWIVEKGIKDVETEDLEDKMETSDIQIFYQEDPECQNLSENSCPPSEVSDTNLYSP FKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQI PVYEQQKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTI PSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVGVGDAKNT DEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISDKFKYIIAQLMR DTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFL YTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESV SRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGI LTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGN VIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKI LHIQTHEKFIRDSQEKPKPVPDKENKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKE CFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATG VQTLYSKWKDFHFEKIPFDPAEMSK
experiment.sample.molecule[0].mw79.77
experiment.sample.molecule[0].total_mw79.77
experiment.sample.molecule[0].number_molecules1
experiment.sample.molecule[0].complex_stateFalse
experiment.sample.molecule[0].deuterationnull
experiment.sample.molecule[0].molecule_sourcebiological
experiment.sample.molecule[0].molecule_descriptionnull
experiment.sample.buffer.name25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.4
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameProbable ATP-dependent RNA helicase DDX58 without CARDs (Delta-CARDs RIG-I)
experiment.sample.ext_coefficientnull
experiment.sample.contrastnull
experiment.sample.specific_volnull
experiment.sample.dry_volnull
experiment.sample.absorbptionnull
experiment.sample.deuterationnull
experiment.sample.mixturenull
experiment.contributor[0].affiliation[0].short_namenull
experiment.contributor[0].affiliation[0].addressMelbourne, Australia
experiment.contributor[0].affiliation[0].full_nameMonash University
experiment.contributor[0].affiliation[0].webpagehttp://www.monash.edu/
experiment.contributor[0].contributor_nameNeelam
experiment.contributor[0].contributor_surnameShah
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2015-05-29
experiment.storage_temperature4.0
experiment.cell_temperature15.0
experiment.exposure_time2.0
experiment.number_of_frames13
experiment.wavelength0.10332
experiment.sample_detector_distance1.6
experiment.concentration_minnull
experiment.concentration_maxnull
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.158
experiment.s_max2.508
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].softwareBUNCH
fits[0].chi_square_value0.68
fits[0].p_value1.8e-05
fits[0].fit_residual_plotSASDBG8_fit1_fitresiduals_img.png
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fits[1].models[0].bead_radius3.5
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fits[1].softwareDAMMIF
fits[1].chi_square_value0.478
fits[1].p_value0.979869
fits[1].fit_residual_plotSASDBG8_fit2_fitresiduals_img.png
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fits[1].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionGNOM v4.5
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of Probable ATP-dependent RNA helicase DDX58 without CARDs (Delta-CARDs RIG-I) in 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, pH 7.4 were collected using size exclusion chromatography (SEC-SAXS) on the SAXS/WAXS camera on the storage ring Australian Synchrotron (Melbourne, Australia) using a Pilatus 1M detector at a sample-detector distance of 1.6 m and at a wavelength of λ = 0.10332 nm (I(s) vs s, where s = 4π sin θ/λ and 2θ is the scattering angle). Data frames (13 x 2 s exposures) were collected through the SEC elution peak at 34.4 min (GE Healthcare Life Sciences Superdex 200 10/300; 0.4 ml/min; 100 μl injection at 8 mg/ml). The data were normalized to the intensity of the transmitted beam and radially averaged; the radially averaged scattering of the solvent-blank was subtracted and the different curves were scaled to yield the final composite scattering curve. The SAXS data were collected at 15 °C.
tags[]
intensity_unitnull
experimental_mw79.7
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw68.5
porod_mw_errornull
pddf_i00.0348
pddf_i0_errornull
guinier_i00.0348
guinier_i0_errornull
pddf_rg3.78
pddf_rg_errornull
guinier_rg3.67
guinier_rg_errornull
pddf_dmax12.98
pddf_dmax_errornull
porod_volume113.99
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first22
guinier_point_last63
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDBG8_datloglog_img.png
symmetrynull
last_modified2019-12-06T13:07:15.624532+01:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDBG8
statussuccess
started_at2026-08-11T15:52:52.168379+00:00
finished_at2026-08-11T15:53:00.748392+00:00
source_last_modified2019-12-06T13:07:15.624532+01:00
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View the complete summary.json source
{
  "code": "SASDBG8",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/A",
  "project": {
    "title": "Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis.",
    "publication": {
      "title": "Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis.",
      "author_list": "Shah N, Beckham SA, Wilce JA, Wilce MCJ",
      "journal": "Nucleic Acids Res",
      "doi": "10.1093/nar/gkx1307",
      "pmid": "29346611",
      "published_date": "2018 Apr 6"
    },
    "status": "released",
    "submitted_date": "2016-12-11",
    "released_date": "2018-01-22"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBG8.out",
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View the complete manifest.json source
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