SASDCY5

Dimeric Sortilin at pH 5.5

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

Sample 1 · Dimeric Sortilin at pH 5.5

Concentration0.0 – 0.62 Buffer / pH25 mM MES pH 5.5, 150 mM NaCl / 5.5
Experimental temperature20.0 Facility / beamlineESRF / BM29
Wavelength0.099 nmExposure1.0 s × 2600

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Sortilin, also: Neurotensin-receptor 3
View sequence
GSGAPAEDQDCGRLPDFIAKLTNNTHQHVFDDLSGSVSLSWVGDSTGVILVLTTFQVPLVIVSFGQSKLYRSEDYGKNFKDITNLINNTFIRTEFGMAIGPENSGKVILTAEVSGGSRGGRVFRSSDFAKNFVQTDLPFHPLTQMMYSPQNSDYLLALSTENGLWVSKNFGEKWEEIHKAVCLAKWGPNNIIFFTTHVNGSCKADLGALELWRTSDLGKTFKTIGVKIYSFGLGGRFLFASVMADKDTTRRIHVSTDQGDTWSMAQLPSVGQEQFYSILAANEDMVFMHVDEPGDTGFGTIFTSDDRGIVYSKSLDRHLYTTTGGETDFTNVTSLRGVYITSTLSEDNSIQSMITFDQGGRWEHLRKPENSKCDATAKNKNECSLHIHASYSISQKLNVPMAPLSEPNAVGIVIAHGSVGDAISVMVPDVYISDDGGYSWAKMLEGPHYYTILDSGGIIVAIEHSNRPINVIKFSTDEGQCWQSYVFTQEPIYFTGLASEPGARSMNISIWGFTESFITRQWVSYTVDFKDILERNCEEDDYTTWLAHSTDPGDYKDGCILGYKEQFLRLRKSSVCQNGRDYVVAKQPSVCPCSLEDFLCDFGYFRPENASECVEQPELKGHELEFCLYGKEEHLTTNGYRKIPGDKCQGGMNPAREVKDLKKKCTSNFLNPTKQNSKSAAAHHHHHH
proteinMus musculusQ6PHU5—–—dimerMolecule count 276.585 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1505[3]0.1269151–2.503451 1/nmHas uncertainty columnMissing 05sasbdb/entries/y5/sasdcy5/source/SASDCY5.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)11.0—nm
i0Guinier53.190.08—
i0P(r)52.90.08—
mwExperimental198.0—kDa
mwGuinier I(0)168.017.0kDa
mwPorod198.0—kDa
porod_volumePorod336.0—nm³
rgGuinier3.890.01nm
rgP(r)3.820.07nm

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 name25 mM MES pH 5.5, 150 mM NaClBuffer concentration—
pH5.5Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2016-04-17Storage / measurement temperature20.0 / 20.0
Exposure time1.0Frames2600
Wavelength0.099Sample-to-detector distance2.87
SourceX-ray synchrotronDetectorPilatus 1M
Facility / beamlineESRF / BM29 · Grenoble, France
q range0.127 – 2.503Sample 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:179 field values
Field pathRaw value
codeSASDCY5
statusPublished
type_of_curveOther
angular_unit1/nm
project.titleLow pH-induced conformational change and dimerization of sortilin triggers endocytosed ligand release.
project.publication.titleLow pH-induced conformational change and dimerization of sortilin triggers endocytosed ligand release.
project.publication.author_listLeloup N, Lössl P, Meijer DH, Brennich M, Heck AJR, Thies-Weesie DME, Janssen BJC
project.publication.journalNat Commun
project.publication.doi10.1038/s41467-017-01485-5
project.publication.pmid29167428
project.publication.published_date2017 Nov 22
project.statusreleased
project.submitted_date2017-07-08
project.released_date2017-12-01
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDCY5.out
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experiment.instrument.detector.typeDectris
experiment.instrument.detector.namePilatus 1M
experiment.instrument.detector.resolution172.0
experiment.instrument.nameESRF
experiment.instrument.cityGrenoble
experiment.instrument.countryFrance
experiment.instrument.beamline_nameBM29
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_nameSortilin, also: Neurotensin-receptor 3
experiment.sample.molecule[0].short_nameSort1, also: NTR3
experiment.sample.molecule[0].sequenceGSGAPAEDQDCGRLPDFIAKLTNNTHQHVFDDLSGSVSLSWVGDSTGVILVLTTFQVPLVIVSFGQSKLYRSEDYGKNFKDITNLINNTFIRTEFGMAIGPENSGKVILTAEVSGGSRGGRVFRSSDFAKNFVQTDLPFHPLTQMMYSPQNSDYLLALSTENGLWVSKNFGEKWEEIHKAVCLAKWGPNNIIFFTTHVNGSCKADLGALELWRTSDLGKTFKTIGVKIYSFGLGGRFLFASVMADKDTTRRIHVSTDQGDTWSMAQLPSVGQEQFYSILAANEDMVFMHVDEPGDTGFGTIFTSDDRGIVYSKSLDRHLYTTTGGETDFTNVTSLRGVYITSTLSEDNSIQSMITFDQGGRWEHLRKPENSKCDATAKNKNECSLHIHASYSISQKLNVPMAPLSEPNAVGIVIAHGSVGDAISVMVPDVYISDDGGYSWAKMLEGPHYYTILDSGGIIVAIEHSNRPINVIKFSTDEGQCWQSYVFTQEPIYFTGLASEPGARSMNISIWGFTESFITRQWVSYTVDFKDILERNCEEDDYTTWLAHSTDPGDYKDGCILGYKEQFLRLRKSSVCQNGRDYVVAKQPSVCPCSLEDFLCDFGYFRPENASECVEQPELKGHELEFCLYGKEEHLTTNGYRKIPGDKCQGGMNPAREVKDLKKKCTSNFLNPTKQNSKSAAAHHHHHH
experiment.sample.molecule[0].organismMus musculus
experiment.sample.molecule[0].uniprot_codeQ6PHU5
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMERPRGAADGLLRWPLGLLLLLQLLPPAAVGQDRLDAPPPPAPPLLRWAGPVGVSWGLRA AAPGGPVPRAGRWRRGAPAEDQDCGRLPDFIAKLTNNTHQHVFDDLSGSVSLSWVGDSTG VILVLTTFQVPLVIVSFGQSKLYRSEDYGKNFKDITNLINNTFIRTEFGMAIGPENSGKV ILTAEVSGGSRGGRVFRSSDFAKNFVQTDLPFHPLTQMMYSPQNSDYLLALSTENGLWVS KNFGEKWEEIHKAVCLAKWGPNNIIFFTTHVNGSCKADLGALELWRTSDLGKTFKTIGVK IYSFGLGGRFLFASVMADKDTTRRIHVSTDQGDTWSMAQLPSVGQEQFYSILAANEDMVF MHVDEPGDTGFGTIFTSDDRGIVYSKSLDRHLYTTTGGETDFTNVTSLRGVYITSTLSED NSIQSMITFDQGGRWEHLRKPENSKCDATAKNKNECSLHIHASYSISQKLNVPMAPLSEP NAVGIVIAHGSVGDAISVMVPDVYISDDGGYSWAKMLEGPHYYTILDSGGIIVAIEHSNR PINVIKFSTDEGQCWQSYVFTQEPIYFTGLASEPGARSMNISIWGFTESFITRQWVSYTV DFKDILERNCEEDDYTTWLAHSTDPGDYKDGCILGYKEQFLRLRKSSVCQNGRDYVVAKQ PSVCPCSLEDFLCDFGYFRPENASECVEQPELKGHELEFCLYGKEEHLTTNGYRKIPGDK CQGGMNPAREVKDLKKKCTSNFLNPTKQNSKSNSVPIILAIVGLMLVTVVAGVLIVKKYV CGGRFLVHRYSVLQQHAEADGVEALDSTSHAKSGYHDDSDEDLLE
experiment.sample.molecule[0].mw76.585
experiment.sample.molecule[0].total_mw153.17
experiment.sample.molecule[0].number_molecules2
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 MES pH 5.5, 150 mM NaCl
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph5.5
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameDimeric Sortilin at pH 5.5
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_nameEMBL
experiment.contributor[0].affiliation[0].addressGrenoble, France
experiment.contributor[0].affiliation[0].full_nameEuropean Molecular Biology Laboratory (EMBL) - Grenoble Outstation
experiment.contributor[0].affiliation[0].webpagehttps://www.embl.fr/
experiment.contributor[0].contributor_nameMartha
experiment.contributor[0].contributor_surnameBrennich
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2016-04-17
experiment.storage_temperature20.0
experiment.cell_temperature20.0
experiment.exposure_time1.0
experiment.number_of_frames2600
experiment.wavelength0.099
experiment.sample_detector_distance2.87
experiment.concentration_min0.0
experiment.concentration_max0.62
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.127
experiment.s_max2.503
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].p_value0.6273
fits[0].fit_residual_plotSASDCY5_fit1_fitresiduals_img.png
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fits[1].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of dimeric sortilin at pH 5.5 in 25 mM MES pH 5.5, 150 mM NaCl, pH 5, were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.099 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Size-exclusion chromatography SAXS (SEC-SAXS) was performed at 20°C where 2600 successive 1 second frames were collected through the elution profile. The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering of an appropriate solvent-blank was subtracted from the SAXS data measured from the sample component elution peaks.
tags[]
intensity_unitnull
experimental_mw198.0
experimental_mw_errornull
guinier_i0_mw168.0
guinier_i0_mw_error17.0
porod_mw198.0
porod_mw_errornull
pddf_i052.9
pddf_i0_error0.08
guinier_i053.19
guinier_i0_error0.08
pddf_rg3.82
pddf_rg_error0.07
guinier_rg3.89
guinier_rg_error0.01
pddf_dmax11.0
pddf_dmax_errornull
porod_volume336.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first1
guinier_point_last45
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDCY5_datloglog_img.png
symmetrynull
last_modified2019-12-06T13:07:15.624532+01:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDCY5
statussuccess
started_at2026-08-11T14:58:55.003749+00:00
finished_at2026-08-11T14:59:04.635782+00:00
source_last_modified2019-12-06T13:07:15.624532+01:00
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View the complete summary.json source
{
  "code": "SASDCY5",
  "status": "Published",
  "type_of_curve": "Other",
  "angular_unit": "1/nm",
  "project": {
    "title": "Low pH-induced conformational change and dimerization of sortilin triggers endocytosed ligand release.",
    "publication": {
      "title": "Low pH-induced conformational change and dimerization of sortilin triggers endocytosed ligand release.",
      "author_list": "Leloup N, Lössl P, Meijer DH, Brennich M, Heck AJR, Thies-Weesie DME, Janssen BJC",
      "journal": "Nat Commun",
      "doi": "10.1038/s41467-017-01485-5",
      "pmid": "29167428",
      "published_date": "2017 Nov 22"
    },
    "status": "released",
    "submitted_date": "2017-07-08",
    "released_date": "2017-12-01"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDCY5.out",
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View the complete manifest.json source
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