{ "code": "SASDVM9", "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/SASDVM9.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVM9.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVM9_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVM9_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVM9_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVM9_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVM9.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Eiger X 1M and Eiger X 9M", "resolution": 75.0 }, "name": "Taiwan Photon Source, NSRRC", "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, "line_collimation_slitlength": null, "line_collimation_integrationwidth": null, "xray_energy": null, "beam_profile_ah": null, "beam_profile_al": null }, "sample": { "molecule": [ { "long_name": "Histone H3.3", "short_name": "H3.3", "sequence": ">\r\nMARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPH", "organism": "Homo sapiens", "uniprot_code": "P84243", "uniprot_range_first": 1, "uniprot_range_last": 40, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTE\nLLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTI\nMPKDIQLARRIRGERA", "mw": 4.189, "total_mw": 8.378, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "" }, { "long_name": "DNA methyltransferase 3-like (178-379)", "short_name": "DNMT3L (178-379)", "sequence": "GHMFETVPVWRRQPVRVLSLFEDIKKELTSLGFLESGSDPGQLKHVVDVTDTVRKDVEEWGPFDLVYGATPPLGHTCDRPPSWYLFQFHRLLQYARPKPGSPRPFFWMFVDNLVLNKEDLDVASRFLEMEPVTIPDVHGGSLQNAVRVWSNIPAIRSRHWALVSEEELSLLAQNKQSSKLAAKWPTKLVKNCFLPLREYFKYFS", "organism": "Homo sapiens", "uniprot_code": "Q9UJW3", "uniprot_range_first": 178, "uniprot_range_last": 379, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MAAIPALDPEAEPSMDVILVGSSELSSSVSPGTGRDLIAYEVKANQRNIEDICICCGSLQ\nVHTQHPLFEGGICAPCKDKFLDALFLYDDDGYQSYCSICCSGETLLICGNPDCTRCYCFE\nCVDSLVGPGTSGKVHAMSNWVCYLCLPSSRSGLLQRRRKWRSQLKAFYDRESENPLEMFE\nTVPVWRRQPVRVLSLFEDIKKELTSLGFLESGSDPGQLKHVVDVTDTVRKDVEEWGPFDL\nVYGATPPLGHTCDRPPSWYLFQFHRLLQYARPKPGSPRPFFWMFVDNLVLNKEDLDVASR\nFLEMEPVTIPDVHGGSLQNAVRVWSNIPAIRSRHWALVSEEELSLLAQNKQSSKLAAKWP\nTKLVKNCFLPLREYFKYFSTELTSSL", "mw": 23.596, "total_mw": 47.192, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "" }, { "long_name": "DNA methyltransferase 3 beta (413-853)", "short_name": "DNMT3B (412-853)", "sequence": "EDQSREQMASDVANNKSSLEDGCLSCGRKNPVSFHPLFEGGLCQTCRDRFLELFYMYDDDGYQSYCTVCCEGRELLLCSNTSCCRCFCVECLEVLVGTGTAAEAKLQEPWSCYMCLPQRCHGVLRRRKDWNVRLQAFFTSDTGLEYEAPKLYPAIPAARRRPIRVLSLFDGIATGYLVLKELGIKVGKYVASEVCEESIAVGTVKHEGNIKYVNDVRNITKKNIEEWGPFDLVIGGSPCNDLSNVNPARKGLYEGTGRLFFEFYHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPVMIDAIKVSAAHRARYFWGNLPGMNRPVIASKNDKLELQDCLEYNRIAKLKKVQTITTKSNSIKQGKNQLFPVVMNGKEDVLWCTELERIFGFPVHYTDVSNMGRGARQKLLGRSWSVPVIRHLFAPLKDYFACE", "organism": "Homo sapiens", "uniprot_code": "Q9UBC3", "uniprot_range_first": 413, "uniprot_range_last": 853, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MKGDTRHLNGEEDAGGREDSILVNGACSDQSSDSPPILEAIRTPEIRGRRSSSRLSKREV\nSSLLSYTQDLTGDGDGEDGDGSDTPVMPKLFRETRTRSESPAVRTRNNNSVSSRERHRPS\nPRSTRGRQGRNHVDESPVEFPATRSLRRRATASAGTPWPSPPSSYLTIDLTDDTEDTHGT\nPQSSSTPYARLAQDSQQGGMESPQVEADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWP\nAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRK\nAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQPVVNKS\nKVRRAGSRKLESRKYENKTRRRTADDSATSDYCPAPKRLKTNCYNNGKDRGDEDQSREQM\nASDVANNKSSLEDGCLSCGRKNPVSFHPLFEGGLCQTCRDRFLELFYMYDDDGYQSYCTV\nCCEGRELLLCSNTSCCRCFCVECLEVLVGTGTAAEAKLQEPWSCYMCLPQRCHGVLRRRK\nDWNVRLQAFFTSDTGLEYEAPKLYPAIPAARRRPIRVLSLFDGIATGYLVLKELGIKVGK\nYVASEVCEESIAVGTVKHEGNIKYVNDVRNITKKNIEEWGPFDLVIGGSPCNDLSNVNPA\nRKGLYEGTGRLFFEFYHLLNYSRPKEGDDRPFFWMFENVVAMKVGDKRDISRFLECNPVM\nIDAIKVSAAHRARYFWGNLPGMNRPVIASKNDKLELQDCLEYNRIAKLKKVQTITTKSNS\nIKQGKNQLFPVVMNGKEDVLWCTELERIFGFPVHYTDVSNMGRGARQKLLGRSWSVPVIR\nHLFAPLKDYFACE", "mw": 50.201, "total_mw": 100.402, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "" } ], "buffer": { "name": "20 mM Tris, 300 mM NaCl, 1 mM TCEP, 5% glycerol", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "Human DNA methyltransferase 3 beta DNMT3B (413-853) and DNA methyltransferase 3-like DNMT3L (178-379) in complex with histone H3", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Taipei, Taiwan", "full_name": "Academia Sinica", "webpage": "https://www.sinica.edu.tw" } ], "contributor_name": "CHAO-CHENG", "contributor_surname": "CHO", "orcid": "" } ], "concentration_method": null, "concentration_unit": null, "date": "2022-11-02", "storage_temperature": 4.0, "cell_temperature": 10.0, "exposure_time": 0.2, "number_of_frames": 113, "wavelength": 0.0827, "sample_detector_distance": 2.515, "concentration_min": null, "concentration_max": 8.0, "sample_volume": null, "flow_rate": null, "s_min": 0.067, "s_max": 5.139, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVM9_fit1_model1_img.png", "software": "GASBOR", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDVM9_fit1_model1.pdb", "model_mw": null, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 1113 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVM9_fit1_fixed_fit_img.png", "software": "GASBOR", "chi_square_value": 1.95, "p_value": 0.0058, "fit_residual_plot": "SASDVM9_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVM9_fit1.fir", "fit_log": null, "software_version": null, "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": null, "experiment_description": null, "tags": [], "intensity_unit": null, "experimental_mw": 156.068, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 115.0, "porod_mw_error": null, "pddf_i0": 0.2118, "pddf_i0_error": null, "guinier_i0": 0.211114, "guinier_i0_error": null, "pddf_rg": 4.58, "pddf_rg_error": null, "guinier_rg": 4.485, "guinier_rg_error": 0.077, "pddf_dmax": 16.02, "pddf_dmax_error": null, "porod_volume": 186.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 50, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDVM9_datloglog_img.png", "symmetry": null, "last_modified": "2025-03-30T18:45:24.168653+02:00", "bragg_peak": [] }