SASDFN3

Complex with 1H histone chaperones Asf1 and Vps75 and histones H3 and H4, 70%-2H histone acetyltransferase Rtt109 (1H Asf1-H3:H4-Vps75, 2H(70%) Rtt109) acquired in 100% v/v D2O

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

Sample 1 · Complex with 1H histone chaperones Asf1 and Vps75 and histones H3 and H4, 70%-2H histone acetyltransferase Rtt109 (1H Asf1-H3:H4-Vps75, 2H(70%) Rtt109) acquired in 100% v/v D2O

Concentration— – 3.8 Buffer / pH50 mM citrate, 150 mM NaCl, 5 mM BME, 100% D2O / 6.5
Experimental temperature25.0 Facility / beamlineFRM2 / KWS1
Wavelength0.5 nmExposure9000.0 s × 1

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Vacuolar protein sorting-associated protein 75 (1-225 aa)
View sequence
MMSDQENENEHAKAFLGLAKCEEEVDAIEREVELYRLNKMKPVYEKRDAYIDEIAEFWKIVLSQHVSFANYIRASDFKYIDTIDKIKVEWLALESEMYDTRDFSITFHFHGIEGDFKEQQVTKVFQIKKGKDDQEDGILTSEPVPIEWPQSYDSINPDLIKDKRSPEGKKKYRQGMKTIFGWFRWTGLKPGKEFPHGDSLASLFSEEIYPFCVKYYAEAQRDLED
proteinSaccharomyces cerevisiaeP538531–225dimerMolecule count 226.554 kDa
Histone acetyltransferase RTT109
View sequence
MSLNDFLSSVLPVSEQFEYLSLQSIPLETHAVVTPNKDDKRVPKSTIKTQHFFSLFHQGKVFFSLEVYVYVTLWDEADAERLIFVSKADTNGYCNTRVSVRDITKIILEFILSIDPNYYLQKVKPAIRSYKKISPELISAASTPARTLRILARRLKQSGSTVLKEIESPRFQQDLYLSFTCPREILTKICLFTRPASQYLFPDSSKNSKKHILNGEELMKWWGFILDRLLIECFQNDTQAKLRIPGEDPARVRSYLRGMKYPLWQVGDIFTSKENSLAVYNIPLFPDDPKARFIHQLAEEDRLLKVSLSSFWIELQERQEFKLSVTSSVMGISGYSLATPSLFPSSADVIVPKSRKQFRAIKKYITGEEYDTEEGAIEAFTNIRDFLLLRMATNLQSLTGKREHRERNQPVPASNINTLAITMLKPRKKAKALPKT
proteinSaccharomyces cerevisiaeQ077941–436monomerMolecule count 150.095 kDa
Histone chaperone ASF1
View sequence
MSIVSLLGIKVLNNPAKFTDPYEFEITFECLESLKHDLEWKLTYVGSSRSLDHDQELDSILVGPVPVGVNKFVFSADPPSAELIPASELVSVTVILLSCSYDGREFVRVGYYVNNEYDEEELRENPPAKVQVDHIVRNILAEKPRVTRFNIVWDNENEGDLYPPEQPGV
protein—P324471–169monomerMolecule count 119.125 kDa
Histone H3.2 (35-135 aa)
View sequence
VKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
proteinXenopus laevisP8423335–135monomerMolecule count 111.747 kDa
Histone H4
View sequence
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
proteinXenopus laevisP627991–103monomerMolecule count 111.367 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1106[3]0.01265196–0.4427638 1/AHas uncertainty columnMissing 018sasbdb/entries/n3/sasdfn3/source/SASDFN3.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)10.5—Å
i0Guinier0.170.00051—
i0P(r)0.167——
mwExperimental96.0—kDa
rgGuinier3.2820.046Å
rgP(r)3.31—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 citrate, 150 mM NaCl, 5 mM BME, 100% D2OBuffer concentration—
pH6.5Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2017-03-04Storage / measurement temperature25.0 / 25.0
Exposure time9000.0Frames1
Wavelength0.5Sample-to-detector distance4.0
Sourceneutron sourceDetector6Li-Scintillator 1 mm thickness + photomultiplier
Facility / beamlineFRM2 / KWS1 · Munich, Germany
q range0.127 – 4.428Sample 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

CategoryFileStatusSizeChecksumDownload and View
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curve:source record
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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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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:227 field values
Field pathRaw value
codeSASDFN3
statusPublished
type_of_curveSingle concentration
angular_unit1/A
project.titleHistone chaperone exploits intrinsic disorder to switch acetylation specificity.
project.publication.titleHistone chaperone exploits intrinsic disorder to switch acetylation specificity.
project.publication.author_listDanilenko N, Lercher L, Kirkpatrick J, Gabel F, Codutti L, Carlomagno T
project.publication.journalNat Commun
project.publication.doi10.1038/s41467-019-11410-7
project.publication.pmid31387991
project.publication.published_date2019 Aug 6
project.statusreleased
project.submitted_date2019-02-27
project.released_date2019-07-10
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDFN3.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDFN3.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFN3_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFN3_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFN3_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFN3_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDFN3.sascif
experiment.instrument.detector.typeSANS
experiment.instrument.detector.name6Li-Scintillator 1 mm thickness + photomultiplier
experiment.instrument.detector.resolution5.3
experiment.instrument.nameFRM2
experiment.instrument.cityMunich
experiment.instrument.countryGermany
experiment.instrument.beamline_nameKWS1
experiment.instrument.beam_geometrynull
experiment.instrument.type_of_sourceneutron source
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_nameVacuolar protein sorting-associated protein 75 (1-225 aa)
experiment.sample.molecule[0].short_nameVps75 1-225
experiment.sample.molecule[0].sequenceMMSDQENENEHAKAFLGLAKCEEEVDAIEREVELYRLNKMKPVYEKRDAYIDEIAEFWKI VLSQHVSFANYIRASDFKYIDTIDKIKVEWLALESEMYDTRDFSITFHFHGIEGDFKEQQ VTKVFQIKKGKDDQEDGILTSEPVPIEWPQSYDSINPDLIKDKRSPEGKKKYRQGMKTIF GWFRWTGLKPGKEFPHGDSLASLFSEEIYPFCVKYYAEAQRDLED
experiment.sample.molecule[0].organismSaccharomyces cerevisiae
experiment.sample.molecule[0].uniprot_codeP53853
experiment.sample.molecule[0].uniprot_range_first1
experiment.sample.molecule[0].uniprot_range_last225
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMMSDQENENEHAKAFLGLAKCEEEVDAIEREVELYRLNKMKPVYEKRDAYIDEIAEFWKI VLSQHVSFANYIRASDFKYIDTIDKIKVEWLALESEMYDTRDFSITFHFHGIEGDFKEQQ VTKVFQIKKGKDDQEDGILTSEPVPIEWPQSYDSINPDLIKDKRSPEGKKKYRQGMKTIF GWFRWTGLKPGKEFPHGDSLASLFSEEIYPFCVKYYAEAQRDLEDEEGESGLSADGDSED DDGSLGEVDLPLSDEEPSSKKRKV
experiment.sample.molecule[0].mw26.554
experiment.sample.molecule[0].total_mw53.108
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.molecule[1].long_nameHistone acetyltransferase RTT109
experiment.sample.molecule[1].short_nameRtt109
experiment.sample.molecule[1].sequenceMSLNDFLSSVLPVSEQFEYLSLQSIPLETHAVVTPNKDDKRVPKSTIKTQHFFSLFHQGK VFFSLEVYVYVTLWDEADAERLIFVSKADTNGYCNTRVSVRDITKIILEFILSIDPNYYL QKVKPAIRSYKKISPELISAASTPARTLRILARRLKQSGSTVLKEIESPRFQQDLYLSFT CPREILTKICLFTRPASQYLFPDSSKNSKKHILNGEELMKWWGFILDRLLIECFQNDTQA KLRIPGEDPARVRSYLRGMKYPLWQVGDIFTSKENSLAVYNIPLFPDDPKARFIHQLAEE DRLLKVSLSSFWIELQERQEFKLSVTSSVMGISGYSLATPSLFPSSADVIVPKSRKQFRA IKKYITGEEYDTEEGAIEAFTNIRDFLLLRMATNLQSLTGKREHRERNQPVPASNINTLA ITMLKPRKKAKALPKT
experiment.sample.molecule[1].organismSaccharomyces cerevisiae
experiment.sample.molecule[1].uniprot_codeQ07794
experiment.sample.molecule[1].uniprot_range_first1
experiment.sample.molecule[1].uniprot_range_last436
experiment.sample.molecule[1].oligomerizationmonomer
experiment.sample.molecule[1].molecular_typeprotein
experiment.sample.molecule[1].uniprot_sequenceMSLNDFLSSVLPVSEQFEYLSLQSIPLETHAVVTPNKDDKRVPKSTIKTQHFFSLFHQGK VFFSLEVYVYVTLWDEADAERLIFVSKADTNGYCNTRVSVRDITKIILEFILSIDPNYYL QKVKPAIRSYKKISPELISAASTPARTLRILARRLKQSGSTVLKEIESPRFQQDLYLSFT CPREILTKICLFTRPASQYLFPDSSKNSKKHILNGEELMKWWGFILDRLLIECFQNDTQA KLRIPGEDPARVRSYLRGMKYPLWQVGDIFTSKENSLAVYNIPLFPDDPKARFIHQLAEE DRLLKVSLSSFWIELQERQEFKLSVTSSVMGISGYSLATPSLFPSSADVIVPKSRKQFRA IKKYITGEEYDTEEGAIEAFTNIRDFLLLRMATNLQSLTGKREHRERNQPVPASNINTLA ITMLKPRKKAKALPKT
experiment.sample.molecule[1].mw50.095
experiment.sample.molecule[1].total_mw50.095
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.molecule[2].long_nameHistone chaperone ASF1
experiment.sample.molecule[2].short_nameAsf1
experiment.sample.molecule[2].sequenceMSIVSLLGIKVLNNPAKFTDPYEFEITFECLESLKHDLEWKLTYVGSSRSLDHDQELDSI LVGPVPVGVNKFVFSADPPSAELIPASELVSVTVILLSCSYDGREFVRVGYYVNNEYDEE ELRENPPAKVQVDHIVRNILAEKPRVTRFNIVWDNENEGDLYPPEQPGV
experiment.sample.molecule[2].organismnull
experiment.sample.molecule[2].uniprot_codeP32447
experiment.sample.molecule[2].uniprot_range_first1
experiment.sample.molecule[2].uniprot_range_last169
experiment.sample.molecule[2].oligomerizationmonomer
experiment.sample.molecule[2].molecular_typeprotein
experiment.sample.molecule[2].uniprot_sequenceMSIVSLLGIKVLNNPAKFTDPYEFEITFECLESLKHDLEWKLTYVGSSRSLDHDQELDSI LVGPVPVGVNKFVFSADPPSAELIPASELVSVTVILLSCSYDGREFVRVGYYVNNEYDEE ELRENPPAKVQVDHIVRNILAEKPRVTRFNIVWDNENEGDLYPPEQPGVDDEEEEDDEEE DDDEDDEDDEDDDQEDGEGEAEEAAEEEEEEEEKTEDNETNLEEEEEDIENSDGDEEEGE EEVGSVDKNEDGNDKKRRKIEGGSTDIESTPKDAARSTN
experiment.sample.molecule[2].mw19.125
experiment.sample.molecule[2].total_mw19.125
experiment.sample.molecule[2].number_molecules1
experiment.sample.molecule[2].complex_stateFalse
experiment.sample.molecule[2].deuterationnull
experiment.sample.molecule[2].molecule_sourcebiological
experiment.sample.molecule[2].molecule_descriptionnull
experiment.sample.molecule[3].long_nameHistone H3.2 (35-135 aa)
experiment.sample.molecule[3].short_nameH3 (35-135)
experiment.sample.molecule[3].sequenceVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAY LVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
experiment.sample.molecule[3].organismXenopus laevis
experiment.sample.molecule[3].uniprot_codeP84233
experiment.sample.molecule[3].uniprot_range_first35
experiment.sample.molecule[3].uniprot_range_last135
experiment.sample.molecule[3].oligomerizationmonomer
experiment.sample.molecule[3].molecular_typeprotein
experiment.sample.molecule[3].uniprot_sequenceMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI MPKDIQLARRIRGERA
experiment.sample.molecule[3].mw11.747
experiment.sample.molecule[3].total_mw11.747
experiment.sample.molecule[3].number_molecules1
experiment.sample.molecule[3].complex_stateFalse
experiment.sample.molecule[3].deuterationnull
experiment.sample.molecule[3].molecule_sourcebiological
experiment.sample.molecule[3].molecule_descriptionnull
experiment.sample.molecule[4].long_nameHistone H4
experiment.sample.molecule[4].short_nameH4
experiment.sample.molecule[4].sequenceMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
experiment.sample.molecule[4].organismXenopus laevis
experiment.sample.molecule[4].uniprot_codeP62799
experiment.sample.molecule[4].uniprot_range_first1
experiment.sample.molecule[4].uniprot_range_last103
experiment.sample.molecule[4].oligomerizationmonomer
experiment.sample.molecule[4].molecular_typeprotein
experiment.sample.molecule[4].uniprot_sequenceMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
experiment.sample.molecule[4].mw11.367
experiment.sample.molecule[4].total_mw11.367
experiment.sample.molecule[4].number_molecules1
experiment.sample.molecule[4].complex_stateFalse
experiment.sample.molecule[4].deuterationnull
experiment.sample.molecule[4].molecule_sourcebiological
experiment.sample.molecule[4].molecule_descriptionnull
experiment.sample.buffer.name50 mM citrate, 150 mM NaCl, 5 mM BME, 100% D2O
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph6.5
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameComplex with 1H histone chaperones Asf1 and Vps75 and histones H3 and H4, 70%-2H histone acetyltransferase Rtt109 (1H Asf1-H3:H4-Vps75, 2H(70%) Rtt109) acquired in 100% v/v D2O
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].addressGermany
experiment.contributor[0].affiliation[0].full_nameLeibniz University of Hannover
experiment.contributor[0].affiliation[0].webpagehttps://www.uni-hannover.de
experiment.contributor[0].contributor_nameNataliya
experiment.contributor[0].contributor_surnameDanilenko
experiment.contributor[0].orcidhttps://orcid.org/0000-0003-4885-5051
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2017-03-04
experiment.storage_temperature25.0
experiment.cell_temperature25.0
experiment.exposure_time9000.0
experiment.number_of_frames1
experiment.wavelength0.5
experiment.sample_detector_distance4.0
experiment.concentration_minnull
experiment.concentration_max3.8
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.127
experiment.s_max4.428
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDFN3_fit1_model1_img.png
fits[0].models[0].softwareHADDOCK
fits[0].models[0].pdb_link[0].pdb_code6o22
fits[0].models[0].pdb_link[0].ext_code6O22
fits[0].models[0].pdb_link[0].ext_typepdb
fits[0].models[0].pdb_link[0].difference_with_modelderived
fits[0].models[0].model_titlenull
fits[0].models[0].type_of_modelatomic
fits[0].models[0].software_versionnull
fits[0].models[0].model_datahttps://www.sasbdb.org/media/pdb_file/SASDFN3_fit1_model1.pdb
fits[0].models[0].model_mw144.0
fits[0].models[0].bead_radiusnull
fits[0].models[0].loghttps://www.sasbdb.org/media/log_files/new190718_12002.log
fits[0].models[0].symmetrynull
fits[0].models[0].commentnull
fits[0].models[0].user420
fits[0].fit_unit1/A
fits[0].fit_plothttps://www.sasbdb.org/media/fitting_files/scattering_plots/new190718_12002_fit_img.png
fits[0].softwareCRYSON
fits[0].chi_square_value2.894
fits[0].p_value0.007065
fits[0].fit_residual_plotnull
fits[0].fit_datahttps://www.sasbdb.org/media/fitting_files/SASDFN3_fit1.fit
fits[0].fit_loghttps://www.sasbdb.org/media/fitting_files/log_files/new190718_12002.log
fits[0].software_versionnull
fits[0].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version4.5a
i0_calibration_standardnull
descriptionnull
experiment_descriptionSANS data from solutions of the Asf1-H3:H4-Rtt109-Vps75 protein complex (1H Asf1-H3:H4-Vps75, bound to 70% 2H-labelled Rtt109) in 50 mM citrate, 150 mM NaCl, 5 mM BME, 100% D2O, pD 6.5 were collected on the KWS1 instrument at FRM2 (Munich, Germany) using a SANS 6Li-Scintillator 1 mm thickness + photomultiplier detector at a sample-detector. The data were recorded at two detector configurations: 1) 4 m for 2.5 hrs using a neutron wavelength of 0.5 nm and; 2) 1.5 m for 2.5 hrs using a neutron wavelength of 0.5 nm. Both measurement were performed on the same sample at 3.8 mg/mL, measured at 25°C.
tags[]
intensity_unitnull
experimental_mw96.0
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manifest.json:36 field values
Field pathRaw value
codeSASDFN3
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View the complete summary.json source
{
  "code": "SASDFN3",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/A",
  "project": {
    "title": "Histone chaperone exploits intrinsic disorder to switch acetylation specificity.",
    "publication": {
      "title": "Histone chaperone exploits intrinsic disorder to switch acetylation specificity.",
      "author_list": "Danilenko N, Lercher L, Kirkpatrick J, Gabel F, Codutti L, Carlomagno T",
      "journal": "Nat Commun",
      "doi": "10.1038/s41467-019-11410-7",
      "pmid": "31387991",
      "published_date": "2019 Aug 6"
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    "status": "released",
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    "released_date": "2019-07-10"
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View the complete manifest.json source
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