SASDBS8

Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) 8mer hairpin dsRNA/ADP-AlFx (SECpeak2)

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 (Full-length RIG-I) 8mer hairpin dsRNA/ADP-AlFx (SECpeak2)

Concentration	— – —	Buffer / pH	25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 2mM ADP-AlFx / 7.4
Experimental temperature	15.0	Facility / beamline	Australian Synchrotron / SAXS/WAXS
Wavelength	0.10332 nm	Exposure	2.0 s × 13

Molecular Components

Component	Type / organism	UniProt and Construct	Oligomeric State	Molecular weight
Probable ATP-dependent RNA helicase DDX58 View sequence MHHHHHHTTEQRRSLQAFQDYIRKTLDPTYILSYMAPWFREEEVQYIQAEKNNKGPMEAATLFLKFLLELQEEGWFRGFLDALDHAGYSGLYEAIESWDFKKIEKLEEYRLLLKRLQPEFKTRIIPTDIISDLSECLINQECEEILQICSTKGMMAGAEKLVECLLRSDKENWPKTLKLALEKERNKFSELWIVEKGIKDVETEDLEDKMETSDIQIFYQEDPECQNLSENSCPPSEVSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQQKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVGVGDAKNTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKILHIQTHEKFIRDSQEKPKPVPDKENKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATGVQTLYSKWKDFHFEKIPFDPAEMSK	proteinHomo sapiens	O957861–925	dimerMolecule count 2	107.421 kDa
5´ppp 8mer hairpin dsRNA View sequence GGCGCGGCUUCGGCCGCGCC	RNA—	—1–20	dimerMolecule count 2	6.484 kDa

Experimental Curves

Curve	Points / columns	q range	Uncertainty quality	Negative-intensity points	Source file
1	565[3]	0.0103427–0.250992 1/A	Has uncertainty columnMissing 0	0	sasbdb/entries/s8/sasdbs8/source/SASDBS8.dat

▼

2. Measurements Reported by SASBDB Reported Results

Metric	Method	Value	Uncertainty	Unit
dmax	P(r)	25.06	—	Å
i0	Guinier	0.0219	—	—
i0	P(r)	0.0222	—	—
mw	Experimental	228.9	—	kDa
mw	Porod	171.0	—	kDa
porod_volume	Porod	298.49	—	Å³
rg	Guinier	5.32	—	Å
rg	P(r)	5.72	—	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

This entry has no source fit record.

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4. Source File Index Source Files

Category	Path	Download status	Size
curve	sasbdb/entries/s8/sasdbs8/source/SASDBS8.dat	downloaded	25425
full_entry_zip	sasbdb/entries/s8/sasdbs8/source/SASDBS8.zip	downloaded	18335
pddf	sasbdb/entries/s8/sasdbs8/source/SASDBS8.out	downloaded	39210
sascif	sasbdb/entries/s8/sasdbs8/source/SASDBS8.sascif	downloaded	64834
summary	sasbdb/entries/s8/sasdbs8/source/summary.json	downloaded	8832

▶

5. Experiment Description and Publication Experiment & Publication

▼

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 name	25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 2mM ADP-AlFx	Buffer concentration	—
pH	7.4	Additives	—
Buffer description	—
Purity measurement method	—	Extinction coefficient	—
Absorbance	—	Scattering contrast	—
Specific volume / dry volume	— / —	Mixture / deuteration	— / —

Acquisition Conditions and Instrument

Measurement date	2015-11-20	Storage / measurement temperature	4.0 / 15.0
Exposure time	2.0	Frames	13
Wavelength	0.10332	Sample-to-detector distance	1.6
Source	X-ray synchrotron	Detector	Pilatus 1M
Facility / beamline	Australian Synchrotron / SAXS/WAXS · Melbourne, Australia
q range	0.103 – 2.51	Sample volume / flow rate	— / —

Original SASBDB Plots

Downloadable Files

Category	File	Status	Size	Checksum	Download and View
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full_entry_zip	sasbdb/entries/s8/sasdbs8/source/SASDBS8.zip	downloaded	18335	3257a13060f1c79ce35d0f4d8096d18e2e51319900260cf7c49ccdf26755d3f3	DownloadView source fileSource site
pddf	sasbdb/entries/s8/sasdbs8/source/SASDBS8.out	downloaded	39210	28fc2edadb44664f5adb37103a65f0ac43891f226a328eb395ab2447fdce1a1a	DownloadView source fileSource site
sascif	sasbdb/entries/s8/sasdbs8/source/SASDBS8.sascif	downloaded	64834	dc571a7cd9fe51df4f96c846370e8f2e816ec808e668b03ab75156a17a4e909c	DownloadView source fileSource site
summary	sasbdb/entries/s8/sasdbs8/source/summary.json	downloaded	8832	cb64b8c7254b543754bdbe99b561b268b12e40ffab2d695b3cba5296ca725a0a	DownloadView source fileSource site

curve：source record

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full_entry_zip：source record and ZIP contents (2 items)

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pddf：source record

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sascif：source record

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summary：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：151 field values

Field path	Raw value
code	SASDBS8
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.
project.publication.title	Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis.
project.publication.author_list	Shah N, Beckham SA, Wilce JA, Wilce MCJ
project.publication.journal	Nucleic Acids Res
project.publication.doi	10.1093/nar/gkx1307
project.publication.pmid	29346611
project.publication.published_date	2018 Apr 6
project.status	released
project.submitted_date	2016-12-11
project.released_date	2018-01-22
pddf_data	https://www.sasbdb.org/media/p_of_R_files/SASDBS8.out
intensities_data	https://www.sasbdb.org/media/intensities_files/SASDBS8.dat
intensities_log_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBS8_dat_img.png
intensities_kratky_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBS8_kratky_img.png
pddf_plot	https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBS8_pofr_img.png
intensities_guinier_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBS8_guinier_img.png
sascif_data	https://www.sasbdb.org/media/sascif/sascif_files/SASDBS8.sascif
experiment.instrument.detector.type	Dectris
experiment.instrument.detector.name	Pilatus 1M
experiment.instrument.detector.resolution	172.0
experiment.instrument.name	Australian Synchrotron
experiment.instrument.city	Melbourne
experiment.instrument.country	Australia
experiment.instrument.beamline_name	SAXS/WAXS
experiment.instrument.beam_geometry	Point
experiment.instrument.type_of_source	X-ray synchrotron
experiment.instrument.point_source	True
experiment.instrument.line_collimation	null
experiment.instrument.sample_path_length	null
experiment.instrument.line_collimation_slitlength	null
experiment.instrument.line_collimation_integrationwidth	null
experiment.instrument.xray_energy	null
experiment.instrument.beam_profile_ah	null
experiment.instrument.beam_profile_al	null
experiment.sample.molecule[0].long_name	Probable ATP-dependent RNA helicase DDX58
experiment.sample.molecule[0].short_name	RIG-I
experiment.sample.molecule[0].sequence	MHHHHHHTTEQRRSLQAFQDYIRKTLDPTYILSYMAPWFREEEVQYIQAEKNNKGPMEAATLFLKFLLELQEEGWFRGFLDALDHAGYSGLYEAIESWDFKKIEKLEEYRLLLKRLQPEFKTRIIPTDIISDLSECLINQECEEILQICSTKGMMAGAEKLVECLLRSDKENWPKTLKLALEKERNKFSELWIVEKGIKDVETEDLEDKMETSDIQIFYQEDPECQNLSENSCPPSEVSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQQKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVGVGDAKNTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKILHIQTHEKFIRDSQEKPKPVPDKENKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATGVQTLYSKWKDFHFEKIPFDPAEMSK
experiment.sample.molecule[0].organism	Homo sapiens
experiment.sample.molecule[0].uniprot_code	O95786
experiment.sample.molecule[0].uniprot_range_first	1
experiment.sample.molecule[0].uniprot_range_last	925
experiment.sample.molecule[0].oligomerization	dimer
experiment.sample.molecule[0].molecular_type	protein
experiment.sample.molecule[0].uniprot_sequence	MTTEQRRSLQAFQDYIRKTLDPTYILSYMAPWFREEEVQYIQAEKNNKGPMEAATLFLKF LLELQEEGWFRGFLDALDHAGYSGLYEAIESWDFKKIEKLEEYRLLLKRLQPEFKTRIIP TDIISDLSECLINQECEEILQICSTKGMMAGAEKLVECLLRSDKENWPKTLKLALEKERN KFSELWIVEKGIKDVETEDLEDKMETSDIQIFYQEDPECQNLSENSCPPSEVSDTNLYSP FKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQI PVYEQQKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTI PSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVGVGDAKNT DEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISDKFKYIIAQLMR DTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFL YTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESV SRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGI LTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGN VIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKI LHIQTHEKFIRDSQEKPKPVPDKENKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKE CFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATG VQTLYSKWKDFHFEKIPFDPAEMSK
experiment.sample.molecule[0].mw	107.421
experiment.sample.molecule[0].total_mw	214.842
experiment.sample.molecule[0].number_molecules	2
experiment.sample.molecule[0].complex_state	False
experiment.sample.molecule[0].deuteration	null
experiment.sample.molecule[0].molecule_source	biological
experiment.sample.molecule[0].molecule_description	null
experiment.sample.molecule[1].long_name	5´ppp 8mer hairpin dsRNA
experiment.sample.molecule[1].short_name	8bp
experiment.sample.molecule[1].sequence	GGCGCGGCUUCGGCCGCGCC
experiment.sample.molecule[1].organism	null
experiment.sample.molecule[1].uniprot_code	null
experiment.sample.molecule[1].uniprot_range_first	1
experiment.sample.molecule[1].uniprot_range_last	20
experiment.sample.molecule[1].oligomerization	dimer
experiment.sample.molecule[1].molecular_type	RNA
experiment.sample.molecule[1].uniprot_sequence	null
experiment.sample.molecule[1].mw	6.484
experiment.sample.molecule[1].total_mw	12.968
experiment.sample.molecule[1].number_molecules	2
experiment.sample.molecule[1].complex_state	False
experiment.sample.molecule[1].deuteration	null
experiment.sample.molecule[1].molecule_source	biological
experiment.sample.molecule[1].molecule_description	null
experiment.sample.buffer.name	25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 2mM ADP-AlFx
experiment.sample.buffer.concentration_unit	null
experiment.sample.buffer.comment	null
experiment.sample.buffer.additive	null
experiment.sample.buffer.concentration	null
experiment.sample.buffer.pka	null
experiment.sample.buffer.ph	7.4
experiment.sample.buffer.deuteration	null
experiment.sample.purity_method	null
experiment.sample.name	Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) 8mer hairpin dsRNA/ADP-AlFx (SECpeak2)
experiment.sample.ext_coefficient	null
experiment.sample.contrast	null
experiment.sample.specific_vol	null
experiment.sample.dry_vol	null
experiment.sample.absorbption	null
experiment.sample.deuteration	null
experiment.sample.mixture	null
experiment.contributor[0].affiliation[0].short_name	null
experiment.contributor[0].affiliation[0].address	Melbourne, Australia
experiment.contributor[0].affiliation[0].full_name	Monash University
experiment.contributor[0].affiliation[0].webpage	http://www.monash.edu/
experiment.contributor[0].contributor_name	Neelam
experiment.contributor[0].contributor_surname	Shah
experiment.contributor[0].orcid	null
experiment.concentration_method	null
experiment.concentration_unit	null
experiment.date	2015-11-20
experiment.storage_temperature	4.0
experiment.cell_temperature	15.0
experiment.exposure_time	2.0
experiment.number_of_frames	13
experiment.wavelength	0.10332
experiment.sample_detector_distance	1.6
experiment.concentration_min	null
experiment.concentration_max	null
experiment.sample_volume	null
experiment.flow_rate	null
experiment.s_min	0.103
experiment.s_max	2.51
experiment.total_exposure_time	null
experiment.seccolumn	null
fits	[]
estimated_volume_method	null
pddf_software	ATSAS GNOM
pddf_software_version	GNOM v4.5
i0_calibration_standard	null
description	null
experiment_description	Synchrotron SAXS data from solutions of Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) 8mer hairpin dsRNA/ADP-AlFx (SECpeak2) in 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, 2mM ADP-AlFx, 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 28.4 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_unit	null
experimental_mw	228.9
experimental_mw_error	null
guinier_i0_mw	null
guinier_i0_mw_error	null
porod_mw	171.0
porod_mw_error	null
pddf_i0	0.0222
pddf_i0_error	null
guinier_i0	0.0219
guinier_i0_error	null
pddf_rg	5.72
pddf_rg_error	null
guinier_rg	5.32
guinier_rg_error	null
pddf_dmax	25.06
pddf_dmax_error	null
porod_volume	298.49
porod_volume_error	null
estimated_volume	null
estimated_volume_error	null
guinier_point_first	10
guinier_point_last	42
pddf_point_first	null
pddf_point_last	null
i0_calibration_standard_data	null
intensities_log_log_plot	SASDBS8_datloglog_img.png
symmetry	null
last_modified	2019-12-06T13:07:15.624532+01:00
bragg_peak	[]

manifest.json：36 field values

Field path	Raw value
code	SASDBS8
status	success
started_at	2026-08-11T15:59:28.837633+00:00
finished_at	2026-08-11T15:59:36.381856+00:00
source_last_modified	2019-12-06T13:07:15.624532+01:00
files[0].status	downloaded
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files[3].role	sascif
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files[4].zip_member_count	2
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View the complete summary.json source

{
  "code": "SASDBS8",
  "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/SASDBS8.out",
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  "last_modified": "2019-12-06T13:07:15.624532+01:00",
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View the complete manifest.json source

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Title	Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis.
Authors	Shah N, Beckham SA, Wilce JA, Wilce MCJ
DOI / PMID	10.1093/nar/gkx1307 / 29346611