SASDF39

Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 - in complex with STAU1 binding site within the ADP-ribosylation factor1

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2020-02-12T18:29:36.378321+01:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 - in complex with STAU1 binding site within the ADP-ribosylation factor1

Concentration— – 3.0 Buffer / pH50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazole / 8.0
Experimental temperature35.0 Facility / beamlineCEITEC / Rigaku BioSAXS-1000
Wavelength0.154 nmExposure600.0 s × 6

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
ADP-ribosylation factor1 - short
View sequence
GGCAGAAGCUGCCUCUUCGGAGGCAGUUUCUGCC
RNAHomo sapiens——–—monomerMolecule count 110.962 kDa
Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4
View sequence
GSHMKSEISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSKKISKKNAAIAVLEELKKLPPLPAVERVKPRIKKKTKPIVKPQTSPEYGQGINPISRLAQIQQAKKEKEPEYTLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFK
proteinHomo sapiensO95793183–355monomerMolecule count 119.733 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1198[3]0.016683–0.300425 1/AHas uncertainty columnMissing 017sasbdb/entries/39/sasdf39/source/SASDF39.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)6.39—Å
i0Guinier0.190.00012arbitrary
i0P(r)0.1882—arbitrary
mwExperimental29.0—kDa
mwPorod24.3—kDa
porod_volumePorod39.0—ų
rgGuinier2.060.036Å
rgP(r)2.03—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

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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 name50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazoleBuffer concentration—
pH8.0Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2018-05-29Storage / measurement temperature20.0 / 35.0
Exposure time600.0Frames6
Wavelength0.154Sample-to-detector distance0.48
SourceX-ray in houseDetectorPilatus 100K
Facility / beamlineCEITEC / Rigaku BioSAXS-1000 · Brno, Czech Republic
q range0.167 – 3.004Sample 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 (4 items)
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pddf: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:173 field values
Field pathRaw value
codeSASDF39
statusPublished
type_of_curveSingle concentration
angular_unit1/A
project.titleStaufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition.
project.publication.titleStaufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition.
project.publication.author_listYadav DK, Zigáčková D, Zlobina M, Klumpler T, Beaumont C, Kubíčková M, Vaňáčová Š, Lukavsky PJ
project.publication.journalNucleic Acids Res
project.publication.doi10.1093/nar/gkz1163
project.publication.pmid31875226
project.publication.published_date2019 Dec 25
project.statusreleased
project.submitted_date2019-07-08
project.released_date2019-11-29
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDF39.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDF39.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF39_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF39_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDF39_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF39_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDF39.sascif
experiment.instrument.detector.typenull
experiment.instrument.detector.namePilatus 100K
experiment.instrument.detector.resolution172.0
experiment.instrument.nameCEITEC
experiment.instrument.cityBrno
experiment.instrument.countryCzech Republic
experiment.instrument.beamline_nameRigaku BioSAXS-1000
experiment.instrument.beam_geometry
experiment.instrument.type_of_sourceX-ray in house
experiment.instrument.point_sourcenull
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_nameADP-ribosylation factor1 - short
experiment.sample.molecule[0].short_nameARF1 RNA - short
experiment.sample.molecule[0].sequenceGGCAGAAGCUGCCUCUUCGGAGGCAGUUUCUGCC
experiment.sample.molecule[0].organismHomo sapiens
experiment.sample.molecule[0].uniprot_codenull
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeRNA
experiment.sample.molecule[0].uniprot_sequencenull
experiment.sample.molecule[0].mw10.962
experiment.sample.molecule[0].total_mw10.962
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.molecule[1].long_nameDouble-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4
experiment.sample.molecule[1].short_nameSTAU1-RBD34
experiment.sample.molecule[1].sequenceGSHMKSEISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSKKISKKNAAIAVLEELKKLPPLPAVERVKPRIKKKTKPIVKPQTSPEYGQGINPISRLAQIQQAKKEKEPEYTLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFK
experiment.sample.molecule[1].organismHomo sapiens
experiment.sample.molecule[1].uniprot_codeO95793
experiment.sample.molecule[1].uniprot_range_first183
experiment.sample.molecule[1].uniprot_range_last355
experiment.sample.molecule[1].oligomerizationmonomer
experiment.sample.molecule[1].molecular_typeprotein
experiment.sample.molecule[1].uniprot_sequenceMSQVQVQVQNPSAALSGSQILNKNQSLLSQPLMSIPSTTSSLPSENAGRPIQNSALPSAS ITSTSAAAESITPTVELNALCMKLGKKPMYKPVDPYSRMQSTYNYNMRGGAYPPRYFYPF PVPPLLYQVELSVGGQQFNGKGKTRQAAKHDAAAKALRILQNEPLPERLEVNGRESEEEN LNKSEISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSKKISKKN AAIAVLEELKKLPPLPAVERVKPRIKKKTKPIVKPQTSPEYGQGINPISRLAQIQQAKKE KEPEYTLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFKVPQAQ PTKPALKSEEKTPIKKPGDGRKVTFFEPGSGDENGTSNKEDEFRMPYLSHQQLPAGILPM VPEVAQAVGVSQGHHTKDFTRAAPNPAKATVTAMIARELLYGGTSPTAETILKNNISSGH VPHGPLTRPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVES CHDMAALNILKLLSELDQQSTEMPRTGNGPMSVCGRC
experiment.sample.molecule[1].mw19.733
experiment.sample.molecule[1].total_mw19.733
experiment.sample.molecule[1].number_molecules1
experiment.sample.molecule[1].complex_stateFalse
experiment.sample.molecule[1].deuterationnull
experiment.sample.molecule[1].molecule_sourcebiological
experiment.sample.molecule[1].molecule_descriptionnull
experiment.sample.buffer.name50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazole
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph8.0
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameDouble-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 - in complex with STAU1 binding site within the ADP-ribosylation factor1
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].addressnull
experiment.contributor[0].affiliation[0].full_nameCEITEC - Central European Institute of Technology, Masaryk University
experiment.contributor[0].affiliation[0].webpagehttps://www.ceitec.eu/
experiment.contributor[0].contributor_nameTomas
experiment.contributor[0].contributor_surnameKlumpler
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2018-05-29
experiment.storage_temperature20.0
experiment.cell_temperature35.0
experiment.exposure_time600.0
experiment.number_of_frames6
experiment.wavelength0.154
experiment.sample_detector_distance0.48
experiment.concentration_minnull
experiment.concentration_max3.0
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.167
experiment.s_max3.004
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].softwareOther
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
fits[0].models[0].type_of_modelatomic
fits[0].models[0].software_versionnull
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fits[0].models[0].model_mw611.6
fits[0].models[0].bead_radiusnull
fits[0].models[0].lognull
fits[0].models[0].symmetrynull
fits[0].models[0].commentnull
fits[0].models[0].user195
fits[0].fit_unit1/A
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fits[0].softwareCRYSOL
fits[0].chi_square_value1.244
fits[0].p_value0.327758
fits[0].fit_residual_plotSASDF39_fit1_fitresiduals_img.png
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fits[0].software_version2.8.3
fits[0].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSAXS data from solutions of double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 - in complex with STAU1 binding site within the ADP-ribosylation factor1 in 50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazole, pH 8 were collected using a Rigaku BioSAXS-1000 instrument (CEITEC; Brno, Czech Republic) equipped with a Pilatus 100K detector at a sample-detector distance of 0.5 m and at a wavelength of λ = 0.154 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.00 mg/ml was measured at 35°C. Six successive 600 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.
tags[]
intensity_unitarbitrary
experimental_mw29.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw24.3
porod_mw_errornull
pddf_i00.1882
pddf_i0_errornull
guinier_i00.19
guinier_i0_error0.00012
pddf_rg2.03
pddf_rg_errornull
guinier_rg2.06
guinier_rg_error0.036
pddf_dmax6.39
pddf_dmax_errornull
porod_volume39.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first1
guinier_point_last33
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDF39_datloglog_img.png
symmetrynull
last_modified2020-02-12T18:29:36.378321+01:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDF39
statussuccess
started_at2026-08-11T16:04:57.375156+00:00
finished_at2026-08-11T16:05:07.336855+00:00
source_last_modified2020-02-12T18:29:36.378321+01:00
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View the complete summary.json source
{
  "code": "SASDF39",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/A",
  "project": {
    "title": "Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition.",
    "publication": {
      "title": "Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition.",
      "author_list": "Yadav DK, Zigáčková D, Zlobina M, Klumpler T, Beaumont C, Kubíčková M, Vaňáčová Š, Lukavsky PJ",
      "journal": "Nucleic Acids Res",
      "doi": "10.1093/nar/gkz1163",
      "pmid": "31875226",
      "published_date": "2019 Dec 25"
    },
    "status": "released",
    "submitted_date": "2019-07-08",
    "released_date": "2019-11-29"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDF39.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDF39.dat",
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  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF39_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDF39_pofr_img.png",
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        "type": null,
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      },
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      "type_of_source": "X-ray in house",
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    },
    "sample": {
      "molecule": [
        {
          "long_name": "ADP-ribosylation factor1 - short",
          "short_name": "ARF1 RNA - short",
          "sequence": "GGCAGAAGCUGCCUCUUCGGAGGCAGUUUCUGCC",
          "organism": "Homo sapiens",
          "uniprot_code": null,
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "monomer",
          "molecular_type": "RNA",
          "uniprot_sequence": null,
          "mw": 10.962,
          "total_mw": 10.962,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
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          "molecule_description": null
        },
        {
          "long_name": "Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4",
          "short_name": "STAU1-RBD34",
          "sequence": "GSHMKSEISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSKKISKKNAAIAVLEELKKLPPLPAVERVKPRIKKKTKPIVKPQTSPEYGQGINPISRLAQIQQAKKEKEPEYTLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFK",
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          "uniprot_code": "O95793",
          "uniprot_range_first": 183,
          "uniprot_range_last": 355,
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          "molecular_type": "protein",
          "uniprot_sequence": "MSQVQVQVQNPSAALSGSQILNKNQSLLSQPLMSIPSTTSSLPSENAGRPIQNSALPSAS\nITSTSAAAESITPTVELNALCMKLGKKPMYKPVDPYSRMQSTYNYNMRGGAYPPRYFYPF\nPVPPLLYQVELSVGGQQFNGKGKTRQAAKHDAAAKALRILQNEPLPERLEVNGRESEEEN\nLNKSEISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSKKISKKN\nAAIAVLEELKKLPPLPAVERVKPRIKKKTKPIVKPQTSPEYGQGINPISRLAQIQQAKKE\nKEPEYTLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFKVPQAQ\nPTKPALKSEEKTPIKKPGDGRKVTFFEPGSGDENGTSNKEDEFRMPYLSHQQLPAGILPM\nVPEVAQAVGVSQGHHTKDFTRAAPNPAKATVTAMIARELLYGGTSPTAETILKNNISSGH\nVPHGPLTRPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVES\nCHDMAALNILKLLSELDQQSTEMPRTGNGPMSVCGRC",
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        }
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        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
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        "deuteration": null
      },
      "purity_method": null,
      "name": "Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 - in complex with STAU1 binding site within the ADP-ribosylation factor1",
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      "contrast": null,
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      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": null,
            "full_name": "CEITEC - Central European Institute of Technology, Masaryk University",
            "webpage": "https://www.ceitec.eu/"
          }
        ],
        "contributor_name": "Tomas",
        "contributor_surname": "Klumpler",
        "orcid": null
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    "concentration_unit": null,
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      "fit_residual_plot": "SASDF39_fit1_fitresiduals_img.png",
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  "symmetry": null,
  "last_modified": "2020-02-12T18:29:36.378321+01:00",
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}
View the complete manifest.json source
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