SASDVJ9

Human DNA methyltransferase 3 beta DNMT3B (215-853) and DNA methyltransferase 3-like DNMT3L (178-379) in complex with histone H3

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2025-03-30T18:45:23.769847+02:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Human DNA methyltransferase 3 beta DNMT3B (215-853) and DNA methyltransferase 3-like DNMT3L (178-379) in complex with histone H3

Concentration— – 5.0 Buffer / pH20 mM Tris, 300 mM NaCl, 1 mM TCEP, 5% glycerol / 8.0
Experimental temperature10.0 Facility / beamlineTaiwan Photon Source, NSRRC / 13A
Wavelength0.0827 nmExposure0.2 s × 199

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Histone H3.3
View sequence
>MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPH
proteinHomo sapiensP842431–40dimerMolecule count 24.189 kDa
DNA methyltransferase 3 beta (215-853)
View sequence
SEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQPVVNKSKVRRAGSRKLESRKYENKTRRRTADDSATSDYCPAPKRLKTNCYNNGKDRGDEDQSREQMASDVANNKSSLEDGCLSCGRKNPVSFHPLFEGGLCQTCRDRFLELFYMYDDDGYQSYCTVCCEGRELLLCSNTSCCRCFCVECLEVLVGTGTAAEAKLQEPWSCYMCLPQRCHGVLRRRKDWNVRLQAFFTSDTGLEYEAPKLYPAIPAARRRPIRVLSLFDGIATGYLVLKELGIKVGKYVASEVCEESIAVGTVKHEGNIKYVNDVRNITKKNIEEWGPFDLVIGGSPCNDLSNVNPARKGLYEGTGRLFFEFYHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPVMIDAIKVSAAHRARYFWGNLPGMNRPVIASKNDKLELQDCLEYNRIAKLKKVQTITTKSNSIKQGKNQLFPVVMNGKEDVLWCTELERIFGFPVHYTDVSNMGRGARQKLLGRSWSVPVIRHLFAPLKDYFACE
proteinHomo sapiensQ9UBC3215–853dimerMolecule count 272.57 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1355[3]0.0–0.54049 1/AHas uncertainty columnMissing 00sasbdb/entries/j9/sasdvj9/source/SASDVJ9.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)18.94—Å
i0Guinier0.168683——
i0P(r)0.1688——
mwExperimental200.798—kDa
mwPorod161.0—kDa
porod_volumePorod275.0—ų
rgGuinier5.1320.553Å
rgP(r)5.22—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 name20 mM Tris, 300 mM NaCl, 1 mM TCEP, 5% glycerolBuffer concentration—
pH8.0Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2021-04-16Storage / measurement temperature4.0 / 10.0
Exposure time0.2Frames199
Wavelength0.0827Sample-to-detector distance2.456
SourceX-ray synchrotronDetectorEiger X 1M and Eiger X 9M
Facility / beamlineTaiwan Photon Source, NSRRC / 13A · Hsinchu, Taiwan
q range0.0 – 5.405Sample 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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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
codeSASDVJ9
statusPublished
type_of_curveSingle concentration
angular_unit1/A
project.titleHistone modification-driven structural remodeling unleashes DNMT3B in DNA methylation.
project.publication.titleHistone modification-driven structural remodeling unleashes DNMT3B in DNA methylation.
project.publication.author_listCho CC, Huang HH, Jiang BC, Yang WZ, Chen YN, Yuan HS
project.publication.journalSci Adv
project.publication.doi10.1126/sciadv.adu8116
project.publication.pmid40138405
project.publication.published_date2025 Mar 28
project.statusreleased
project.submitted_date2024-11-09
project.released_date2025-01-25
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDVJ9.out
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sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDVJ9.sascif
experiment.instrument.detector.typenull
experiment.instrument.detector.nameEiger X 1M and Eiger X 9M
experiment.instrument.detector.resolution75.0
experiment.instrument.nameTaiwan Photon Source, NSRRC
experiment.instrument.cityHsinchu
experiment.instrument.countryTaiwan
experiment.instrument.beamline_name13A
experiment.instrument.beam_geometrynull
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_nameHistone H3.3
experiment.sample.molecule[0].short_nameH3.3
experiment.sample.molecule[0].sequence> MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPH
experiment.sample.molecule[0].organismHomo sapiens
experiment.sample.molecule[0].uniprot_codeP84243
experiment.sample.molecule[0].uniprot_range_first1
experiment.sample.molecule[0].uniprot_range_last40
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTE LLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTI MPKDIQLARRIRGERA
experiment.sample.molecule[0].mw4.189
experiment.sample.molecule[0].total_mw8.378
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_description
experiment.sample.molecule[1].long_nameDNA methyltransferase 3 beta (215-853)
experiment.sample.molecule[1].short_nameDNMT3B (215-853)
experiment.sample.molecule[1].sequenceSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQPVVNKSKVRRAGSRKLESRKYENKTRRRTADDSATSDYCPAPKRLKTNCYNNGKDRGDEDQSREQMASDVANNKSSLEDGCLSCGRKNPVSFHPLFEGGLCQTCRDRFLELFYMYDDDGYQSYCTVCCEGRELLLCSNTSCCRCFCVECLEVLVGTGTAAEAKLQEPWSCYMCLPQRCHGVLRRRKDWNVRLQAFFTSDTGLEYEAPKLYPAIPAARRRPIRVLSLFDGIATGYLVLKELGIKVGKYVASEVCEESIAVGTVKHEGNIKYVNDVRNITKKNIEEWGPFDLVIGGSPCNDLSNVNPARKGLYEGTGRLFFEFYHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPVMIDAIKVSAAHRARYFWGNLPGMNRPVIASKNDKLELQDCLEYNRIAKLKKVQTITTKSNSIKQGKNQLFPVVMNGKEDVLWCTELERIFGFPVHYTDVSNMGRGARQKLLGRSWSVPVIRHLFAPLKDYFACE
experiment.sample.molecule[1].organismHomo sapiens
experiment.sample.molecule[1].uniprot_codeQ9UBC3
experiment.sample.molecule[1].uniprot_range_first215
experiment.sample.molecule[1].uniprot_range_last853
experiment.sample.molecule[1].oligomerizationdimer
experiment.sample.molecule[1].molecular_typeprotein
experiment.sample.molecule[1].uniprot_sequenceMKGDTRHLNGEEDAGGREDSILVNGACSDQSSDSPPILEAIRTPEIRGRRSSSRLSKREV SSLLSYTQDLTGDGDGEDGDGSDTPVMPKLFRETRTRSESPAVRTRNNNSVSSRERHRPS PRSTRGRQGRNHVDESPVEFPATRSLRRRATASAGTPWPSPPSSYLTIDLTDDTEDTHGT PQSSSTPYARLAQDSQQGGMESPQVEADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWP AMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRK AMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQPVVNKS KVRRAGSRKLESRKYENKTRRRTADDSATSDYCPAPKRLKTNCYNNGKDRGDEDQSREQM ASDVANNKSSLEDGCLSCGRKNPVSFHPLFEGGLCQTCRDRFLELFYMYDDDGYQSYCTV CCEGRELLLCSNTSCCRCFCVECLEVLVGTGTAAEAKLQEPWSCYMCLPQRCHGVLRRRK DWNVRLQAFFTSDTGLEYEAPKLYPAIPAARRRPIRVLSLFDGIATGYLVLKELGIKVGK YVASEVCEESIAVGTVKHEGNIKYVNDVRNITKKNIEEWGPFDLVIGGSPCNDLSNVNPA RKGLYEGTGRLFFEFYHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPVM IDAIKVSAAHRARYFWGNLPGMNRPVIASKNDKLELQDCLEYNRIAKLKKVQTITTKSNS IKQGKNQLFPVVMNGKEDVLWCTELERIFGFPVHYTDVSNMGRGARQKLLGRSWSVPVIR HLFAPLKDYFACE
experiment.sample.molecule[1].mw72.57
experiment.sample.molecule[1].total_mw145.14
experiment.sample.molecule[1].number_molecules2
experiment.sample.molecule[1].complex_stateFalse
experiment.sample.molecule[1].deuterationnull
experiment.sample.molecule[1].molecule_sourcebiological
experiment.sample.molecule[1].molecule_description
experiment.sample.buffer.name20 mM Tris, 300 mM NaCl, 1 mM TCEP, 5% glycerol
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
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experiment.sample.buffer.pkanull
experiment.sample.buffer.ph8.0
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameHuman DNA methyltransferase 3 beta DNMT3B (215-853) and DNA methyltransferase 3-like DNMT3L (178-379) in complex with histone H3
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].addressTaipei, Taiwan
experiment.contributor[0].affiliation[0].full_nameAcademia Sinica
experiment.contributor[0].affiliation[0].webpagehttps://www.sinica.edu.tw
experiment.contributor[0].contributor_nameCHAO-CHENG
experiment.contributor[0].contributor_surnameCHO
experiment.contributor[0].orcid
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2021-04-16
experiment.storage_temperature4.0
experiment.cell_temperature10.0
experiment.exposure_time0.2
experiment.number_of_frames199
experiment.wavelength0.0827
experiment.sample_detector_distance2.456
experiment.concentration_minnull
experiment.concentration_max5.0
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.0
experiment.s_max5.405
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].user1113
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fits[0].softwareGASBOR
fits[0].chi_square_value1.05
fits[0].p_value0.3129
fits[0].fit_residual_plotSASDVJ9_fit1_fitresiduals_img.png
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fits[0].description
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pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionnull
tags[]
intensity_unitnull
experimental_mw200.798
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw161.0
porod_mw_errornull
pddf_i00.1688
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guinier_i0_errornull
pddf_rg5.22
pddf_rg_errornull
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guinier_rg_error0.553
pddf_dmax18.94
pddf_dmax_errornull
porod_volume275.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first34
guinier_point_last63
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDVJ9_datloglog_img.png
symmetrynull
last_modified2025-03-30T18:45:23.769847+02:00
bragg_peak[]
manifest.json:34 field values
Field pathRaw value
codeSASDVJ9
statussuccess
started_at2026-08-11T16:46:08.255666+00:00
finished_at2026-08-11T16:46:15.367864+00:00
source_last_modified2025-03-30T18:45:23.769847+02:00
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View the complete summary.json source
{
  "code": "SASDVJ9",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/A",
  "project": {
    "title": "Histone modification-driven structural remodeling unleashes DNMT3B in DNA methylation.",
    "publication": {
      "title": "Histone modification-driven structural remodeling unleashes DNMT3B in DNA methylation.",
      "author_list": "Cho CC, Huang HH, Jiang BC, Yang WZ, Chen YN, Yuan HS",
      "journal": "Sci Adv",
      "doi": "10.1126/sciadv.adu8116",
      "pmid": "40138405",
      "published_date": "2025 Mar 28"
    },
    "status": "released",
    "submitted_date": "2024-11-09",
    "released_date": "2025-01-25"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDVJ9.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVJ9.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVJ9_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVJ9_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVJ9_pofr_img.png",
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        "resolution": 75.0
      },
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      "city": "Hsinchu",
      "country": "Taiwan",
      "beamline_name": "13A",
      "beam_geometry": null,
      "type_of_source": "X-ray synchrotron",
      "point_source": null,
      "line_collimation": null,
      "sample_path_length": null,
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      "line_collimation_integrationwidth": null,
      "xray_energy": null,
      "beam_profile_ah": null,
      "beam_profile_al": null
    },
    "sample": {
      "molecule": [
        {
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View the complete manifest.json source
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