SASDFK8

GON7, the fifth subunit of human KEOPS

Data type: SASBDB experimental data Status: Published Curve type: SEC-SAS Last updated: 2022-01-26T20:16:52.725524+01:00

The scattered intensities were displayed on an absolute scale (cm-1) using the scattering of water. SAXS data were normalized to the intensity of the incident beam, averaged and background subtracted using the program US-SOMO. Frames were examined individually and 30 identical frames were averaged and further processed. The corresponding SEC-elution concentration was approximately 1.5 mg/mL.

▼

1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · GON7, the fifth subunit of human KEOPS

Concentration— – 6.7 Buffer / pH20 mM MES, 200 mM NaCl, 5 mM β-mercaptoethanol / 6.5
Experimental temperature15.0 Facility / beamlineSOLEIL / SWING
Wavelength0.1 nmExposure1.0 s × 255

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
EKC/KEOPS complex subunit GON7
View sequence
MGHHHHHHENLYFQGELLGEYVGQEGKPQKLRVSCEAPGDGDPFQGLLSGVAQMKDMVTELFDPLVQGEVQHRVAAAPDEDLDGDDEDDAEDENNIDNRTNFDGPSAKRPKTPS
proteinHomo sapiensQ9BXV92–100monomerMolecule count 112.59 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1874[3]0.00958007320091–0.500271777004 1/AHas uncertainty columnMissing 00sasbdb/entries/k8/sasdfk8/source/SASDFK8.dat
▼

2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)12.5—Å
i0Guinier0.019714e-051/cm
i0P(r)0.01988—1/cm
mwExperimental14.7—kDa
mwGuinier I(0)14.7—kDa
mwPorod29.0—kDa
porod_volumePorod46.0—ų
rgGuinier3.080.01Å
rgP(r)3.25—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.

▶

4. Source File Index Source Files

▶

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 name20 mM MES, 200 mM NaCl, 5 mM β-mercaptoethanolBuffer concentration—
pH6.5Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2017-03-26Storage / measurement temperature— / 15.0
Exposure time1.0Frames255
Wavelength0.1Sample-to-detector distance1.8
SourceX-ray synchrotronDetectorAVIEX PCCD170170
Facility / beamlineSOLEIL / SWING · Saint-Aubin, France
q range0.096 – 5.003Sample volume / flow rate65.0 / 0.3

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:134 field values
Field pathRaw value
codeSASDFK8
statusPublished
type_of_curveSEC-SAS
angular_unit1/A
project.titleDefects in t<sup>6</sup>A tRNA modification due to GON7 and YRDC mutations lead to Galloway-Mowat syndrome.
project.publication.titleDefects in t<sup>6</sup>A tRNA modification due to GON7 and YRDC mutations lead to Galloway-Mowat syndrome.
project.publication.author_listArrondel C, Missoury S, Snoek R, Patat J, Menara G, Collinet B, Liger D, Durand D, Gribouval O, Boyer O, Buscara L, Martin G, Machuca E, Nevo F, Lescop E, Braun DA, Boschat AC, Sanquer S, Guerrera IC, Revy P, Parisot M, Masson C, Boddaert N, Charbit M, Decramer S, Novo R, Macher MA, Ranchin B, Bacchetta J, Laurent A, Collardeau-Frachon S, van Eerde AM, Hildebrandt F, Magen D, Antignac C, van Tilbeurgh H, Mollet G
project.publication.journalNat Commun
project.publication.doi10.1038/s41467-019-11951-x
project.publication.pmid31481669
project.publication.published_date2019 Sep 3
project.statusreleased
project.submitted_date2019-07-05
project.released_date2019-09-05
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sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDFK8.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_nameEKC/KEOPS complex subunit GON7
experiment.sample.molecule[0].short_nameGON7
experiment.sample.molecule[0].sequenceMGHHHHHHENLYFQGELLGEYVGQEGKPQKLRVSCEAPGDGDPFQGLLSGVAQMKDMVTELFDPLVQGEVQHRVAAAPDEDLDGDDEDDAEDENNIDNRTNFDGPSAKRPKTPS
experiment.sample.molecule[0].organismHomo sapiens
experiment.sample.molecule[0].uniprot_codeQ9BXV9
experiment.sample.molecule[0].uniprot_range_first2
experiment.sample.molecule[0].uniprot_range_last100
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMELLGEYVGQEGKPQKLRVSCEAPGDGDPFQGLLSGVAQMKDMVTELFDPLVQGEVQHRV AAAPDEDLDGDDEDDAEDENNIDNRTNFDGPSAKRPKTPS
experiment.sample.molecule[0].mw12.59
experiment.sample.molecule[0].total_mw12.59
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.buffer.name20 mM MES, 200 mM NaCl, 5 mM β-mercaptoethanol
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.nameGON7, the fifth subunit of human KEOPS
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].addressParis, France
experiment.contributor[0].affiliation[0].full_nameI2BC-CNRS
experiment.contributor[0].affiliation[0].webpagehttp://www.i2bc.paris-saclay.fr
experiment.contributor[0].contributor_namesophia
experiment.contributor[0].contributor_surnamemissoury
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2017-03-26
experiment.storage_temperaturenull
experiment.cell_temperature15.0
experiment.exposure_time1.0
experiment.number_of_frames255
experiment.wavelength0.1
experiment.sample_detector_distance1.8
experiment.concentration_minnull
experiment.concentration_max6.7
experiment.sample_volume65.0
experiment.flow_rate0.3
experiment.s_min0.096
experiment.s_max5.003
experiment.total_exposure_timenull
experiment.seccolumn10
fits[]
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionThe scattered intensities were displayed on an absolute scale (cm-1) using the scattering of water. SAXS data were normalized to the intensity of the incident beam, averaged and background subtracted using the program US-SOMO. Frames were examined individually and 30 identical frames were averaged and further processed. The corresponding SEC-elution concentration was approximately 1.5 mg/mL.
experiment_descriptionSynchrotron SAXS data from solutions of GON7 in 20 mM MES, 200 mM NaCl, 5 mM β-mercaptoethanol, pH 6.5 were collected on the SWING beam line at SOLEIL (Saint-Aubin, France) using a AVIEX PCCD170170 detector at a sample-detector distance of 1.8 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 65.00 μl sample at 6.7 mg/ml was injected at a 0.30 ml/min flow rate onto a Agilent Bio SEC-3, 300 Å column at 15°C. 255 successive 1 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[0]idp
intensity_unit1/cm
experimental_mw14.7
experimental_mw_errornull
guinier_i0_mw14.7
guinier_i0_mw_errornull
porod_mw29.0
porod_mw_errornull
pddf_i00.01988
pddf_i0_errornull
guinier_i00.01971
guinier_i0_error4e-05
pddf_rg3.25
pddf_rg_errornull
guinier_rg3.08
guinier_rg_error0.01
pddf_dmax12.5
pddf_dmax_errornull
porod_volume46.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first5
guinier_point_last47
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDFK8_datloglog_img.png
symmetrynull
last_modified2022-01-26T20:16:52.725524+01:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDFK8
statussuccess
started_at2026-08-11T15:55:03.504045+00:00
finished_at2026-08-11T15:55:11.238408+00:00
source_last_modified2022-01-26T20:16:52.725524+01:00
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View the complete summary.json source
{
  "code": "SASDFK8",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/A",
  "project": {
    "title": "Defects in t<sup>6</sup>A tRNA modification due to GON7 and YRDC mutations lead to Galloway-Mowat syndrome.",
    "publication": {
      "title": "Defects in t<sup>6</sup>A tRNA modification due to GON7 and YRDC mutations lead to Galloway-Mowat syndrome.",
      "author_list": "Arrondel C, Missoury S, Snoek R, Patat J, Menara G, Collinet B, Liger D, Durand D, Gribouval O, Boyer O, Buscara L, Martin G, Machuca E, Nevo F, Lescop E, Braun DA, Boschat AC, Sanquer S, Guerrera IC, Revy P, Parisot M, Masson C, Boddaert N, Charbit M, Decramer S, Novo R, Macher MA, Ranchin B, Bacchetta J, Laurent A, Collardeau-Frachon S, van Eerde AM, Hildebrandt F, Magen D, Antignac C, van Tilbeurgh H, Mollet G",
      "journal": "Nat Commun",
      "doi": "10.1038/s41467-019-11951-x",
      "pmid": "31481669",
      "published_date": "2019 Sep 3"
    },
    "status": "released",
    "submitted_date": "2019-07-05",
    "released_date": "2019-09-05"
  },
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  "tags": [
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  "guinier_point_last": 47,
  "pddf_point_first": null,
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  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDFK8_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2022-01-26T20:16:52.725524+01:00",
  "bragg_peak": []
}
View the complete manifest.json source
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