Semi-synthetic nucleosome core particle (NCP) in complex with lysine-specific demethylase (LSD2) and the dehydrogenase domain plus linker of cytokine-like nuclear factor (NPAC delta-205)

{
  "code": "SASDFY3",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/nm",
  "project": {
    "title": "A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex.",
    "publication": {
      "title": "A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex.",
      "author_list": "Marabelli C, Marrocco B, Pilotto S, Chittori S, Picaud S, Marchese S, Ciossani G, Forneris F, Filippakopoulos P, Schoehn G, Rhodes D, Subramaniam S, Mattevi A",
      "journal": "Cell Rep",
      "doi": "10.1016/j.celrep.2019.03.061",
      "pmid": "30970244",
      "published_date": "2019 Apr 9"
    },
    "status": "released",
    "submitted_date": "2019-03-12",
    "released_date": "2019-04-16"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFY3.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFY3.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFY3_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFY3_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFY3_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFY3_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFY3.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": "Dectris",
        "name": "Pilatus 1M",
        "resolution": 172.0
      },
      "name": "ESRF",
      "city": "Grenoble",
      "country": "France",
      "beamline_name": "BM29",
      "beam_geometry": "",
      "type_of_source": "X-ray synchrotron",
      "point_source": null,
      "line_collimation": null,
      "sample_path_length": null,
      "line_collimation_slitlength": null,
      "line_collimation_integrationwidth": null,
      "xray_energy": null,
      "beam_profile_ah": null,
      "beam_profile_al": null
    },
    "sample": {
      "molecule": [
        {
          "long_name": "Lysyne-specific Demethylase LSD2",
          "short_name": "LSD2",
          "sequence": "KKKATETTDEDEDGGSEKKYRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEH\r\nFCNECFDHYYRSHKDGYDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPECRKW\r\nRQLTKEIQLTPQIAKTYRCGMKPNTAIKPETSDHCSLPEDLRVLEVSNHWWYSMLILPPL\r\nLKDSVAAPLLSAYYPDCVGMSPSCTSTNRAAATGNASPGKLEHSKAALSVHVPGMNRYFQ\r\nPFYQPNECGKALCVRPDVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEALTPQK\r\nCIPHIIVRGLVRIRCVQEVERILYFMTRKGLINTGVLSVGADQYLLPKDYHNKSVIIIGA\r\nGPAGLAAARQLHNFGIKVTVLEAKDRIGGRVWDDKSFKGVTVGRGAQIVNGCINNPVALM\r\nCEQLGISMHKFGERCDLIQEGGRITDPTIDKRMDFHFNALLDVVSEWRKDKTQLQDVPLG\r\nEKIEEIYKAFIKESGIQFSELEGQVLQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAG\r\nDHTLLTPGYSVIIEKLAEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLVTVPLA\r\nLLQKGAIQFNPPLSEKKMKAINSLGAGIIEKIALQFPYRFWDSKVQGADFFGHVPPSASK\r\nRGLFAVFYDMDPQKKHSVLMSVIAGEAVASVRTLDDKQVLQQCMATLRELFKEQEVPDPT\r\nKYFVTRWSTDPWIQMAYSFVKTGGSGEAYDIIAEDIQGTVFFAGEATNRHFPQTVTGAYL\r\nSGVREASKIAAF",
          "organism": "Homo sapiens",
          "uniprot_code": "Q8NB78",
          "uniprot_range_first": 31,
          "uniprot_range_last": 822,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "MATPRGRTKKKASFDHSPDSLPLRSSGRQAKKKATETTDEDEDGGSEKKYRKCEKAGCTA\nTCPVCFASASERCAKNGYTSRWYHLSCGEHFCNECFDHYYRSHKDGYDKYTTWKKIWTSN\nGKTEPSPKAFMADQQLPYWVQCTKPECRKWRQLTKEIQLTPQIAKTYRCGMKPNTAIKPE\nTSDHCSLPEDLRVLEVSNHWWYSMLILPPLLKDSVAAPLLSAYYPDCVGMSPSCTSTNRA\nAATGNASPGKLEHSKAALSVHVPGMNRYFQPFYQPNECGKALCVRPDVMELDELYEFPEY\nSRDPTMYLALRNLILALWYTNCKEALTPQKCIPHIIVRGLVRIRCVQEVERILYFMTRKG\nLINTGVLSVGADQYLLPKDYHNKSVIIIGAGPAGLAAARQLHNFGIKVTVLEAKDRIGGR\nVWDDKSFKGVTVGRGAQIVNGCINNPVALMCEQLGISMHKFGERCDLIQEGGRITDPTID\nKRMDFHFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESGIQFSELEGQVLQFHL\nSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLLTPGYSVIIEKLAEGLDIQLKSPVQC\nIDYSGDEVQVTTTDGTGYSAQKVLVTVPLALLQKGAIQFNPPLSEKKMKAINSLGAGIIE\nKIALQFPYRFWDSKVQGADFFGHVPPSASKRGLFAVFYDMDPQKKHSVLMSVIAGEAVAS\nVRTLDDKQVLQQCMATLRELFKEQEVPDPTKYFVTRWSTDPWIQMAYSFVKTGGSGEAYD\nIIAEDIQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAAF",
          "mw": 88.832,
          "total_mw": 88.832,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        },
        {
          "long_name": "NPAC linker+DH (delta-205)",
          "short_name": "NPAC delta205",
          "sequence": "TASEPVKDADPHFHHFLLSQTEKPAVCYQAITKKLKICEEETGSTSIQAADSTAVNGSIT\r\nPTDKKIGFLGLGLMGSGIVSNLLKMGHTVTVWNRTAEKCDLFIQEGARLGRTPAEVVSTC\r\nDITFACVSDPKAAKDLVLGPSGVLQGIRPGKCYVDMSTVDADTVTELAQVIVSRGGRFLE\r\nAPVSGNQQLSNDGMLVILAAGDRGLYEDCSSCFQAMGKTSFFLGEVGNAAKMMLIVNMVQ\r\nGSFMATIAEGLTLAQVTGQSQQTLLDILNQGQLASIFLDQKCQNILQGNFKPDFYLKYIQ\r\nKDLRLAIALGDAVNHPTPMAAAANEVYKRAKALDQSDNDMSAVYRAYIH",
          "organism": "Homo sapiens",
          "uniprot_code": "Q49A26",
          "uniprot_range_first": 205,
          "uniprot_range_last": 553,
          "oligomerization": "tetramer",
          "molecular_type": "protein",
          "uniprot_sequence": "MAAVSLRLGDLVWGKLGRYPPWPGKIVNPPKDLKKPRGKKCFFVKFFGTEDHAWIKVEQL\nKPYHAHKEEMIKINKGKRFQQAVDAVEEFLRRAKGKDQTSSHNSSDDKNRRNSSEERSRP\nNSGDEKRKLSLSEGKVKKNMGEGKKRVSSGSSERGSKSPLKRAQEQSPRKRGRPPKDEKD\nLTIPESSTVKGMMAGPMAAFKWQPTASEPVKDADPHFHHFLLSQTEKPAVCYQAITKKLK\nICEEETGSTSIQAADSTAVNGSITPTDKKIGFLGLGLMGSGIVSNLLKMGHTVTVWNRTA\nEKCDLFIQEGARLGRTPAEVVSTCDITFACVSDPKAAKDLVLGPSGVLQGIRPGKCYVDM\nSTVDADTVTELAQVIVSRGGRFLEAPVSGNQQLSNDGMLVILAAGDRGLYEDCSSCFQAM\nGKTSFFLGEVGNAAKMMLIVNMVQGSFMATIAEGLTLAQVTGQSQQTLLDILNQGQLASI\nFLDQKCQNILQGNFKPDFYLKYIQKDLRLAIALGDAVNHPTPMAAAANEVYKRAKALDQS\nDNDMSAVYRAYIH",
          "mw": 37.438,
          "total_mw": 149.752,
          "number_molecules": 4,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        },
        {
          "long_name": "Histone H3",
          "short_name": "H3",
          "sequence": "ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR\r\nLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA",
          "organism": "Xenopus laevis",
          "uniprot_code": null,
          "uniprot_range_first": 2,
          "uniprot_range_last": 136,
          "oligomerization": "dimer",
          "molecular_type": "protein",
          "uniprot_sequence": null,
          "mw": 15.271,
          "total_mw": 30.542,
          "number_molecules": 2,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        },
        {
          "long_name": "Histone H4",
          "short_name": "H4",
          "sequence": "SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDA\r\nVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG",
          "organism": "Xenopus laevis",
          "uniprot_code": "P62799",
          "uniprot_range_first": 2,
          "uniprot_range_last": 103,
          "oligomerization": "dimer",
          "molecular_type": "protein",
          "uniprot_sequence": "MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK\nVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG",
          "mw": 11.236,
          "total_mw": 22.472,
          "number_molecules": 2,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        },
        {
          "long_name": "Histone H2a",
          "short_name": "H2a",
          "sequence": "SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNA\r\nARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK",
          "organism": "Xenopus laevis",
          "uniprot_code": "Q6AZJ8",
          "uniprot_range_first": 2,
          "uniprot_range_last": 130,
          "oligomerization": "dimer",
          "molecular_type": "protein",
          "uniprot_sequence": "MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT\nAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK\nTESSKSAKSK",
          "mw": 13.95,
          "total_mw": 27.9,
          "number_molecules": 2,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        },
        {
          "long_name": "Histone H2b",
          "short_name": "H2b",
          "sequence": "AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFER\r\nIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK",
          "organism": "Xenopus laevis",
          "uniprot_code": "Q92130",
          "uniprot_range_first": 5,
          "uniprot_range_last": 126,
          "oligomerization": "dimer",
          "molecular_type": "protein",
          "uniprot_sequence": "MPDPAKSAPAAKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAM\nSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT\nKYTSAK",
          "mw": 13.494,
          "total_mw": 26.988,
          "number_molecules": 2,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        },
        {
          "long_name": "147bp 601 Widom sequence",
          "short_name": "601-147bp",
          "sequence": "ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCGAT",
          "organism": "synthetic construct",
          "uniprot_code": null,
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "monomer",
          "molecular_type": "DNA",
          "uniprot_sequence": null,
          "mw": 45.202,
          "total_mw": 45.202,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "15 mM HEPES, 200 mM NaCl",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.3,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Semi-synthetic nucleosome core particle (NCP) in complex with lysine-specific demethylase (LSD2) and the dehydrogenase domain plus linker of cytokine-like nuclear factor (NPAC delta-205)",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "Italy",
            "full_name": "University of Pavia",
            "webpage": "http://wcm-3.unipv.it"
          }
        ],
        "contributor_name": "Federico",
        "contributor_surname": "Forneris",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2017-12-11",
    "storage_temperature": 4.0,
    "cell_temperature": 20.0,
    "exposure_time": 1.0,
    "number_of_frames": 70,
    "wavelength": 0.1,
    "sample_detector_distance": 2.87,
    "concentration_min": null,
    "concentration_max": 1.8,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.081,
    "s_max": 2.862,
    "total_exposure_time": null,
    "seccolumn": null
  },
  "fits": [],
  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": "5.0",
  "i0_calibration_standard": null,
  "description": null,
  "experiment_description": "Synchrotron SAXS data from solutions of a semi-synthetic nucleosome core particle (NCP) in complex with lysine-specific demethylase (LSD2) and truncated cytokine-like nuclear factor (NPAC delta-205) in 15 mM HEPES, 200 mM NaCl, pH 7.3 were collected using size-exclusion chromatography SAXS (SEC-SAXS) 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 = 0.1 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). SEC-SAXS was performed at 20 °C using the following parameters: Column: Wyatt WTC-030N5; Flow rate: 0.25 mL/min; Sample injection concentration: 3 mg/mL; Injection volume: 50 μL. The data were collected through the SEC peak of the sample as a series of 70 x 1 second exposures. Each unsubtracted data frame was normalised to the intensity of the transmitted beam and radially averaged and the scattering of an appropriate solvent-blank was subtracted. The resulting subtracted frames were scaled and averaged to generate the final SAXS profile displayed in this entry.",
  "tags": [],
  "intensity_unit": "arbitrary",
  "experimental_mw": 530.0,
  "experimental_mw_error": null,
  "guinier_i0_mw": null,
  "guinier_i0_mw_error": null,
  "porod_mw": null,
  "porod_mw_error": null,
  "pddf_i0": 162.2,
  "pddf_i0_error": null,
  "guinier_i0": 157.8,
  "guinier_i0_error": 0.2,
  "pddf_rg": 8.396,
  "pddf_rg_error": null,
  "guinier_rg": 7.84,
  "guinier_rg_error": 0.01,
  "pddf_dmax": 30.35,
  "pddf_dmax_error": null,
  "porod_volume": 1100.0,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 2,
  "guinier_point_last": 25,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDFY3_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
  "bragg_peak": []
}

{
  "code": "SASDFY3",
  "status": "success",
  "started_at": "2026-08-11T14:10:54.843558+00:00",
  "finished_at": "2026-08-11T14:11:01.725612+00:00",
  "source_last_modified": "2019-12-06T13:07:15.624532+01:00",
  "files": [
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/rest-api/entry/summary/SASDFY3/",
      "path": "/data/saxsdb/sasbdb/entries/y3/sasdfy3/source/summary.json",
      "size": 13817,
      "sha256": "82af47d4a1d16ab1f2de406b7cd6e4ede22762f01eddf37328dff65de1d75fe8"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/intensities_files/SASDFY3.dat",
      "path": "/data/saxsdb/sasbdb/entries/y3/sasdfy3/source/SASDFY3.dat",
      "size": 27340,
      "sha256": "2f6aeac491e3cd5ce28c4f7da27d1031e56b481abe20c0f198386ad1323aaa3c",
      "role": "curve"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/p_of_R_files/SASDFY3.out",
      "path": "/data/saxsdb/sasbdb/entries/y3/sasdfy3/source/SASDFY3.out",
      "size": 23116,
      "sha256": "9e649a8dd01e8bd94025c6d3578969745a90b9023de8d01aa4e271435be5e9c7",
      "role": "pddf"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFY3.sascif",
      "path": "/data/saxsdb/sasbdb/entries/y3/sasdfy3/source/SASDFY3.sascif",
      "size": 7207,
      "sha256": "9776518fea4bd8912ee9d92ab9fd041b939419c453b458ba3dcd451dd619c145",
      "role": "sascif"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/zip_directories/SASDFY3.zip",
      "path": "/data/saxsdb/sasbdb/entries/y3/sasdfy3/source/SASDFY3.zip",
      "size": 15372,
      "sha256": "ff6ecca5b5491dee36cc8949a7d2a83d66768537dfb625c8255e96ceb87243e1",
      "role": "full_entry_zip",
      "zip_member_count": 2,
      "zip_validation": "central_directory_readable"
    }
  ]
}