Ser48-phosphorylated N-terminal domain of transactive response DNA-binding protein 43 (TDP-43)

{
  "code": "SASDV74",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/A",
  "project": {
    "title": "Semi-synthesis of TDP-43 reveals the effects of phosphorylation in N-terminal domain on self-association",
    "publication": {
      "title": "Semi-synthesis of TDP-43 reveals the effects of phosphorylation in N-terminal domain on self-association",
      "author_list": "Sasaki D, Tenda M, Sohma Y",
      "journal": "Communications Chemistry",
      "doi": "10.1038/s42004-025-01522-1",
      "pmid": null,
      "published_date": "2025 Apr 25"
    },
    "status": "released",
    "submitted_date": "2024-07-05",
    "released_date": "2025-04-29"
  },
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  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDV74_kratky_img.png",
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  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDV74_guinier_img.png",
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  "experiment": {
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      "detector": {
        "type": null,
        "name": "Pilatus3 S 2M",
        "resolution": 172.0
      },
      "name": "SPring-8",
      "city": "Hyogo prefecture",
      "country": "Japan",
      "beamline_name": "BL38B1",
      "beam_geometry": null,
      "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": "TAR DNA-binding protein 43",
          "short_name": "TDP-43",
          "sequence": "MSEYIRVTEDENDEPIEIPSEDDGTVLLSTVTAQFPGACGLRYRNPVSQCMRGVRLVEGILHAPDAGWGNLVYVVNYPKD",
          "organism": "Homo sapiens",
          "uniprot_code": "Q13148",
          "uniprot_range_first": 1,
          "uniprot_range_last": 80,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "MSEYIRVTEDENDEPIEIPSEDDGTVLLSTVTAQFPGACGLRYRNPVSQCMRGVRLVEGI\nLHAPDAGWGNLVYVVNYPKDNKRKMDETDASSAVKVKRAVQKTSDLIVLGLPWKTTEQDL\nKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNS\nKQSQDEPLRSRKVFVGRCTEDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIA\nQSLCGEDLIIKGISVHISNAEPKHNSNRQLERSGRFGGNPGGFGNQGGFGNSRGGGAGLG\nNNQGSNMGGGMNFGAFSINPAMMAAAQAALQSSWGMMGMLASQQNQSGPSGNNQNQGNMQ\nREPNQAFGSGNNSYSGSNSGAAIGWGSASNAGSGSGFNGGFGSSMDSKSSGWGM",
          "mw": 8.869,
          "total_mw": 8.869,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": "Ser48 is phosphorylated."
        }
      ],
      "buffer": {
        "name": "50 mM Tris-HCl, 150 mM NaCl, 1 mM DTT, 3% glycerol",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 8.5,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Ser48-phosphorylated N-terminal domain of transactive response DNA-binding protein 43 (TDP-43)",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": null,
            "full_name": "Wakayama Medical University",
            "webpage": null
          }
        ],
        "contributor_name": "Daisuke",
        "contributor_surname": "Sasaki",
        "orcid": "https://orcid.org/0000-0002-2224-1900"
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2024-05-29",
    "storage_temperature": 5.0,
    "cell_temperature": 20.0,
    "exposure_time": 3.0,
    "number_of_frames": 28,
    "wavelength": 0.1,
    "sample_detector_distance": 2.4,
    "concentration_min": null,
    "concentration_max": 9.0,
    "sample_volume": 200.0,
    "flow_rate": 0.3,
    "s_min": 0.154,
    "s_max": 4.611,
    "total_exposure_time": null,
    "seccolumn": 3
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          "symmetry": "P1",
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      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDV74_fit1_fixed_fit_img.png",
      "software": "DAMMIF",
      "chi_square_value": 1.459,
      "p_value": 0.0292,
      "fit_residual_plot": "SASDV74_fit1_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDV74_fit1.fir",
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      "description": ""
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          "software": "Other",
          "pdb_link": [],
          "model_title": null,
          "type_of_model": "atomic",
          "software_version": "NMATOR",
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          "bead_radius": null,
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          "symmetry": "P1",
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      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDV74_fit2_fixed_fit_img.png",
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      "chi_square_value": 1.623,
      "p_value": 0.0009,
      "fit_residual_plot": "SASDV74_fit2_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDV74_fit2.fit",
      "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/pk1_bth_A_cn_m9.log",
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  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": "5.0",
  "i0_calibration_standard": null,
  "description": "The dummy atom models shown in this entry (DAM) represent: 1) Top: the minimised spatial alignment of several individual models that have undergone subsequent volume and bead-occupancy correction (DAMFILT model) and 2) Bottom: an individual DAM model example and corresponding fit to the data. The entire DAMMIF model cohort (20 individual models) are made available in the full entry zip archive.",
  "experiment_description": "Synchrotron in-line size exclusion chromatography (SEC)-SAXS data for solution of Ser48-phosphorylated N-terminal domain of TDP-43 in 50 mM Tris-HCl, 150 mM NaCl, 1 mM DTT, 3% glycerol, pH 8.5 were collected on the BL38B1 beam line at SPring-8 (Hyogo prefecture, Japan) using a PILATUS 3 S 2M detector at a sample-detector distance of 2.4 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). The SEC conditions were as follows; A 200 μL sample at a concentration of 9 mg/mL was injected onto a Superdex 75 Increase 10/300 column (GE) at 20°C and eluted at a flow rate of 0.3 mL/min. Successive 28 frames (3 sec exposure per frame) within the SEC elution peak were extracted and used for averaging. The data were normalized to the intensity of the transmitted beam and radially averaged. The scattering from the solvent background was subtracted.",
  "tags": [],
  "intensity_unit": "1/cm",
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  "guinier_i0_mw_error": null,
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  "guinier_rg_error": 0.059,
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  "pddf_dmax_error": null,
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  "estimated_volume_error": null,
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  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
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  "symmetry": null,
  "last_modified": "2025-04-30T14:22:19.324274+02:00",
  "bragg_peak": []
}

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  "started_at": "2026-08-11T14:15:42.493809+00:00",
  "finished_at": "2026-08-11T14:15:56.740591+00:00",
  "source_last_modified": "2025-04-30T14:22:19.324274+02:00",
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