SASDA89

Complex between ovine GM-CSF and GM-CSF/IL-2 inhibition factor

Data type: SASBDB experimental data Status: Published Curve type: Other Last updated: 2019-12-06T13:07:15.624532+01:00

Modeling of SAXS data: The crystal structure of the GIF:oGM-CSF complex was used as an input for the Allosmod-FoXS web server to model missing loops, N- and C-termini and N-linked glycosylation. During each Allosmod-FoXS run, data up to a scattering angle of 0.5 Å-1 was used. Fits to the experimental SAXS data were calculated using the FoXS software.

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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Complex between ovine GM-CSF and GM-CSF/IL-2 inhibition factor

Concentration— – 9.7 mg/mlBuffer / pH20 mM HEPES 150 mM NaCl / 7.4
Experimental temperature20.0 Facility / beamlineSOLEIL / SWING
Wavelength0.1 nmExposure— s × 16

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
GM-CSF/IL-2 inhibition factor
View sequence
MACLRVFLAVLALCGSVHSAQWIGERDFCTAHAQDVFARLQVWMRIDRNVTAADNSSACALAIETPPSNFDADVYVAAAGINVSVSAINCGFFNMRQVETTYNTARRQMYVYMDSWDPWVIDDPQPLFSQEYENETLPYLLEVLELARLYIRVGCTVPGEQPFEVIPGIDYPHTGMEFLQHVLRPNRRFAPAKLHMDLEVDHRCVSAVHVKAFLQDACSARKARTPLYFAGHGCNHPDRRPKNPVPRPQHVSSPISRKCSMQTAR
proteinOrf virusQ9J5U5—–—tetramerMolecule count 429.924 kDa
Granulocyte-macrophage colony-stimulating factor
View sequence
APTRQPSPVTRPWQHVDAIKEALSLLNDSTDTAAVMDETVEVVSEMFDSQEPTCLQTRLELYKQGLRGSLTSLTGSLTMMASHYKKHCPPTQETSCETQIITFKSFKENLKDFLFIIPFDCWEPVQK
proteinOvis ariesP2877318–144dimerMolecule count 214.411 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11073[3]0.07607809–5.496227 1/nmHas uncertainty columnMissing 02sasbdb/entries/89/sasda89/source/SASDA89.dat
▼

2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)12.4—nm
i0Guinier0.1513810.0001—
i0P(r)0.1494——
mwExperimental153.0—kDa
mwGuinier I(0)153.0—kDa
mwPorod144.0—kDa
porod_volumePorod231.0—nm³
rgGuinier3.790.13nm
rgP(r)3.77—nm

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

▶

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 name20 mM HEPES 150 mM NaClBuffer concentration20.0 mM
pH7.4Additives150 mM NaCl
Buffer description—
Purity measurement methodSEC-SAXSExtinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2014-09-10Storage / measurement temperature— / 20.0
Exposure time—Frames16
Wavelength0.1Sample-to-detector distance1.82
SourceX-ray synchrotronDetectorAVIEX PCCD170170
Facility / beamlineSOLEIL / SWING · Saint-Aubin, France
q range0.076 – 5.496Sample 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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All source fields (unfiltered)

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

summary.json:170 field values
Field pathRaw value
codeSASDA89
statusPublished
type_of_curveOther
angular_unit1/nm
project.titleStructural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF.
project.publication.titleStructural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF.
project.publication.author_listFelix J, Kandiah E, De Munck S, Bloch Y, van Zundert GC, Pauwels K, Dansercoer A, Novanska K, Read RJ, Bonvin AM, Vergauwen B, Verstraete K, Gutsche I, Savvides SN
project.publication.journalNat Commun
project.publication.doi10.1038/ncomms13228
project.publication.pmid27819269
project.publication.published_date2016 Nov 7
project.statusreleased
project.submitted_date2015-08-07
project.released_date2016-12-16
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDA89.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDA89.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDA89_dat_img.png
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pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDA89_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDA89_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDA89.sascif
experiment.instrument.detector.typeCCD
experiment.instrument.detector.nameAVIEX PCCD170170
experiment.instrument.detector.resolutionnull
experiment.instrument.nameSOLEIL
experiment.instrument.citySaint-Aubin
experiment.instrument.countryFrance
experiment.instrument.beamline_nameSWING
experiment.instrument.beam_geometry
experiment.instrument.type_of_sourceX-ray synchrotron
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_nameGM-CSF/IL-2 inhibition factor
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequenceMACLRVFLAVLALCGSVHSAQWIGERDFCTAHAQDVFARLQVWMRIDRNVTAADNSSACALAIETPPSNFDADVYVAAAGINVSVSAINCGFFNMRQVETTYNTARRQMYVYMDSWDPWVIDDPQPLFSQEYENETLPYLLEVLELARLYIRVGCTVPGEQPFEVIPGIDYPHTGMEFLQHVLRPNRRFAPAKLHMDLEVDHRCVSAVHVKAFLQDACSARKARTPLYFAGHGCNHPDRRPKNPVPRPQHVSSPISRKCSMQTAR
experiment.sample.molecule[0].organismOrf virus
experiment.sample.molecule[0].uniprot_codeQ9J5U5
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationtetramer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMACLRVFLAVLALCGSVHSAQWIGERDFCTAHAQDVFARLQVWMRIDRNVTAADNSSACA LAIETPPSNFDADVYVAAAGINVSVSAINCGFFNMRQVETTYNTARRQMYVYMDSWDPWV IDDPQPLFSQEYENETLPYLLEVLELARLYIRVGCTVPGEQPFEVIPGIDYPHTGMEFLQ HVLRPNRRFAPAKLHMDLEVDHRCVSAVHVKAFLQDACSARKARTPLYFAGHGCNHPDRR PKNPVPRPQHVSSPISRKCSMQTAR
experiment.sample.molecule[0].mw29.924
experiment.sample.molecule[0].total_mw119.696
experiment.sample.molecule[0].number_molecules4
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_nameGranulocyte-macrophage colony-stimulating factor
experiment.sample.molecule[1].short_namenull
experiment.sample.molecule[1].sequenceAPTRQPSPVTRPWQHVDAIKEALSLLNDSTDTAAVMDETVEVVSEMFDSQEPTCLQTRLE LYKQGLRGSLTSLTGSLTMMASHYKKHCPPTQETSCETQIITFKSFKENLKDFLFIIPFD CWEPVQK
experiment.sample.molecule[1].organismOvis aries
experiment.sample.molecule[1].uniprot_codeP28773
experiment.sample.molecule[1].uniprot_range_first18
experiment.sample.molecule[1].uniprot_range_last144
experiment.sample.molecule[1].oligomerizationdimer
experiment.sample.molecule[1].molecular_typeprotein
experiment.sample.molecule[1].uniprot_sequenceMWLQNLLLLGTVVCSFSAPTRQPSPVTRPWQHVDAIKEALSLLNDSTDTAAVMDETVEVV SEMFDSQEPTCLQTRLELYKQGLRGSLTSLTGSLTMMASHYKKHCPPTQETSCETQIITF KSFKENLKDFLFIIPFDCWEPVQK
experiment.sample.molecule[1].mw14.411
experiment.sample.molecule[1].total_mw28.823
experiment.sample.molecule[1].number_molecules2
experiment.sample.molecule[1].complex_stateTrue
experiment.sample.molecule[1].deuterationnull
experiment.sample.molecule[1].molecule_sourcebiological
experiment.sample.molecule[1].molecule_descriptionnull
experiment.sample.buffer.name20 mM HEPES 150 mM NaCl
experiment.sample.buffer.concentration_unitmM
experiment.sample.buffer.commentnull
experiment.sample.buffer.additive150 mM NaCl
experiment.sample.buffer.concentration20.0
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.4
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodSEC-SAXS
experiment.sample.nameComplex between ovine GM-CSF and GM-CSF/IL-2 inhibition factor
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[]
experiment.contributor[0].contributor_nameJan
experiment.contributor[0].contributor_surnameFelix
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitmg/ml
experiment.date2014-09-10
experiment.storage_temperaturenull
experiment.cell_temperature20.0
experiment.exposure_timenull
experiment.number_of_frames16
experiment.wavelength0.1
experiment.sample_detector_distance1.82
experiment.concentration_minnull
experiment.concentration_max9.7
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.076
experiment.s_max5.496
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].softwareFoXS
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
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fits[0].models[0].bead_radius1.9
fits[0].models[0].lognull
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fits[0].models[0].comment
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fits[0].softwarenull
fits[0].chi_square_value99.0
fits[0].p_value0.0
fits[0].fit_residual_plotSASDA89_fit1_fitresiduals_img.png
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fits[0].fit_lognull
fits[0].software_versionnull
fits[0].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionnull
i0_calibration_standardnull
descriptionModeling of SAXS data: The crystal structure of the GIF:oGM-CSF complex was used as an input for the Allosmod-FoXS web server to model missing loops, N- and C-termini and N-linked glycosylation. During each Allosmod-FoXS run, data up to a scattering angle of 0.5 Å-1 was used. Fits to the experimental SAXS data were calculated using the FoXS software.
experiment_descriptionX-ray synchrotron radiation scattering data from solutions of the complex between GM-CSF/IL-2 inhibition factor and ovine Granulocyte-macrophage colony-stimulating factor in 20 mM HEPES 150 mM NaCl were collected on the SWING camera on the storage ring SOLEIL (Saint-Aubin, France) using a CCD AVIEX detector (I(s) vs s, where s = 4π sin θ/λ, where 2θ is the scattering angle). One solute concentration of 10 mg/ml was measured. 10 successive 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 and the different curves were scaled for protein concentration. The purity of the sample was obtained via SEC-SAXS.
tags[]
intensity_unitnull
experimental_mw153.0
experimental_mw_errornull
guinier_i0_mw153.0
guinier_i0_mw_errornull
porod_mw144.0
porod_mw_errornull
pddf_i00.1494
pddf_i0_errornull
guinier_i00.151381
guinier_i0_error0.0001
pddf_rg3.77
pddf_rg_errornull
guinier_rg3.79
guinier_rg_error0.13
pddf_dmax12.4
pddf_dmax_errornull
porod_volume231.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first17
guinier_point_last47
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDA89_datloglog_img.png
symmetrynull
last_modified2019-12-06T13:07:15.624532+01:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDA89
statussuccess
started_at2026-08-11T16:08:07.778449+00:00
finished_at2026-08-11T16:08:23.035116+00:00
source_last_modified2019-12-06T13:07:15.624532+01:00
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View the complete summary.json source
{
  "code": "SASDA89",
  "status": "Published",
  "type_of_curve": "Other",
  "angular_unit": "1/nm",
  "project": {
    "title": "Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF.",
    "publication": {
      "title": "Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF.",
      "author_list": "Felix J, Kandiah E, De Munck S, Bloch Y, van Zundert GC, Pauwels K, Dansercoer A, Novanska K, Read RJ, Bonvin AM, Vergauwen B, Verstraete K, Gutsche I, Savvides SN",
      "journal": "Nat Commun",
      "doi": "10.1038/ncomms13228",
      "pmid": "27819269",
      "published_date": "2016 Nov 7"
    },
    "status": "released",
    "submitted_date": "2015-08-07",
    "released_date": "2016-12-16"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDA89.out",
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  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDA89.sascif",
  "experiment": {
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        "type": "CCD",
        "name": "AVIEX PCCD170170",
        "resolution": null
      },
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      "city": "Saint-Aubin",
      "country": "France",
      "beamline_name": "SWING",
      "beam_geometry": "",
      "type_of_source": "X-ray synchrotron",
      "point_source": null,
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    },
    "sample": {
      "molecule": [
        {
          "long_name": "GM-CSF/IL-2 inhibition factor",
          "short_name": null,
          "sequence": "MACLRVFLAVLALCGSVHSAQWIGERDFCTAHAQDVFARLQVWMRIDRNVTAADNSSACALAIETPPSNFDADVYVAAAGINVSVSAINCGFFNMRQVETTYNTARRQMYVYMDSWDPWVIDDPQPLFSQEYENETLPYLLEVLELARLYIRVGCTVPGEQPFEVIPGIDYPHTGMEFLQHVLRPNRRFAPAKLHMDLEVDHRCVSAVHVKAFLQDACSARKARTPLYFAGHGCNHPDRRPKNPVPRPQHVSSPISRKCSMQTAR",
          "organism": "Orf virus",
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        "comment": null,
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      "absorbption": null,
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    "contributor": [
      {
        "affiliation": [],
        "contributor_name": "Jan",
        "contributor_surname": "Felix",
        "orcid": null
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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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