{"code":"SASDFT8","status":"Published","type_of_curve":"SEC-SAS","angular_unit":"1/A","project":{"title":"Structural basis for DNA recognition and allosteric control of the retinoic acid receptors RAR–RXR","publication":{"title":"Structural basis for DNA recognition and allosteric control of the retinoic acid receptors RAR–RXR","author_list":"Osz J, McEwen A, Bourguet M, Przybilla F, Peluso-Iltis C, Poussin-Courmontagne P, Mély Y, Cianférani S, Jeffries C, Svergun D, Rochel N","journal":"Nucleic Acids Research","doi":"10.1093/nar/gkaa697","pmid":null,"published_date":"2020 Aug 25"},"status":"released","submitted_date":"2020-06-24","released_date":"2020-08-11"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDFT8.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDFT8.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFT8_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFT8_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFT8_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFT8_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDFT8.sascif","experiment":{"instrument":{"detector":{"type":null,"name":"Pilatus 2M","resolution":null},"name":"PETRA III","city":"DESY; Hamburg","country":"Germany","beamline_name":"EMBL P12","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":"Retinoic acid receptor alpha, RAR","short_name":"mRARa","sequence":"MGSSHHHHHHSSGLVPRGSHMIYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFDVGMSKESVRNDRNKKKKEAPKPECSESYTLTPEVGELIEKVRKAHQETFPALCQLGKYTTNNSSEQRVSLDIDLWDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHNAGFGPLTDLVFAFANQLLPLEMDDAETGLLSAICLICGDRQDLEQPDKVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSISAKGAERVITLKMEIPGSMPPLIQEMLENSEGLD","organism":"Mus musculus","uniprot_code":"P11416","uniprot_range_first":84,"uniprot_range_last":421,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MASNSSSCPTPGGGHLNGYPVPPYAFFFPPMLGGLSPPGALTSLQHQLPVSGYSTPSPAT\nIETQSSSSEEIVPSPPSPPPLPRIYKPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNM\nVYTCHRDKNCIINKVTRNRCQYCRLQKCFDVGMSKESVRNDRNKKKKEAPKPECSESYTL\nTPEVGELIEKVRKAHQETFPALCQLGKYTTNNSSEQRVSLDIDLWDKFSELSTKCIIKTV\nEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHNA\nGFGPLTDLVFAFANQLLPLEMDDAETGLLSAICLICGDRQDLEQPDKVDMLQEPLLEALK\nVYVRKRRPSRPHMFPKMLMKITDLRSISAKGAERVITLKMEIPGSMPPLIQEMLENSEGL\nDTLSGQSGGGTRDGGGLAPPPGSCSPSLSPSSHRSSPATQSP","mw":40.786,"total_mw":40.786,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null},{"long_name":"Retinoic acid receptor RXR-alpha","short_name":"mRXRa","sequence":"FTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDRNENEVESTSSANEDMPVEKILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAPHQAT","organism":"Mus musculus","uniprot_code":"P28700","uniprot_range_first":135,"uniprot_range_last":467,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MDTKHFLPLDFSTQVNSSSLNSPTGRGSMAVPSLHPSLGPGIGSPLGSPGQLHSPISTLS\nSPINGMGPPFSVISSPMGPHSMSVPTTPTLGFGTGSPQLNSPMNPVSSTEDIKPPLGLNG\nVLKVPAHPSGNMASFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNK\nDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDRNENEVESTSSANEDMPVEKI\nLEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLD\nDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVS\nKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRF\nAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAPHQAT","mw":37.745,"total_mw":37.745,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null},{"long_name":"DNA response element HoxB13 DR0","short_name":"HoxB13 DR0","sequence":"GAAGGTCAAGGCCAAG\r\nCTTCCAGTTCCGGTTC","organism":null,"uniprot_code":null,"uniprot_range_first":null,"uniprot_range_last":null,"oligomerization":"monomer","molecular_type":"DNA","uniprot_sequence":null,"mw":9.905,"total_mw":9.905,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null}],"buffer":{"name":"20 mM Tris, pH 8, 150 mM NaCl, 5% v/v glycerol, 1 mM CHAPS, 4 mM MgSO4, 1 mM TCEP","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":8.0,"deuteration":null},"purity_method":null,"name":"The retinoic acid receptor (RAR-RXR heterodimer) bound to the DNA response element HoxB13 DR0","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":"EMBL-Hamburg","address":"Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany","full_name":"European Molecular Biology Laboratory (EMBL) - Hamburg outstation","webpage":"http://www.embl-hamburg.de/index.php"}],"contributor_name":"Cy M","contributor_surname":"Jeffries","orcid":null}],"concentration_method":null,"concentration_unit":null,"date":"2014-01-19","storage_temperature":20.0,"cell_temperature":10.0,"exposure_time":1.0,"number_of_frames":45,"wavelength":0.124,"sample_detector_distance":3.0,"concentration_min":null,"concentration_max":5.5,"sample_volume":100.0,"flow_rate":0.5,"s_min":0.02,"s_max":4.512,"total_exposure_time":null,"seccolumn":1},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDFT8_fit1_model1_img.png","software":"CORAL","pdb_link":[],"model_title":null,"type_of_model":"mix","software_version":"5","model_data":"https://www.sasbdb.org/media/pdb_file/SASDFT8_fit1_model1.pdb","model_mw":87.02,"bead_radius":null,"log":"https://www.sasbdb.org/media/log_files/crysol_summary_FqDsEYb.txt","symmetry":"P1","comment":null,"user":9}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDFT8_fit1_fixed_fit_img.png","software":"CRYSOL","chi_square_value":1.25,"p_value":0.0332,"fit_residual_plot":"SASDFT8_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDFT8_fit1.fit","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/RARRXRHoxb13Csaxs00.log","software_version":null,"description":"CRYSOL fit of a CORAL model repersentative"}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"4.6","i0_calibration_standard":null,"description":"SEC-SAXS analysis was performed in parallel with right-angle laser light scattering (RALLS) and refractive index measurements at room temperature. The Rg-correlation through the SEC-SAXS peak, as well as the results from coupled RALLS/RI, and alternative CORAL rigid-body refined models that fit the scattering data are included in the full entry zip archive. The quoted experimental molecular weight was determined from RALLS/RI measurements that were recorded from the same sample eluting from the column using a split-flow SEC-SAXS-light scattering configuration  as described in Graewert et al., (2015) Sci. Reports. 5, 10734: doi: 10.1038/srep10734. The MW estimated directly from the SAXS data using Bayesian inference is ca. 86 kDa in the interval 81-93 kDa (Hajizadeh et al., (2018) Sci. Reports. 8(1):7204. doi: 10.1038/s41598-018-25355-2).","experiment_description":"Synchrotron SAXS data from solutions of the retinoic acid receptor (RXR/RAR heterodimer) bound to the DNA response element HoxB13 DR0 in 20 mM Tris, pH 8, 150 mM NaCl, 5% v/v glycerol, 1 mM CHAPS, 4 mM MgSO4, 1 mM TCEP were collected on the EMBL P12 beam line at PETRA III (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 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 100.00 μl sample at 5.5 mg/ml was injected at a 0.50 ml/min flow rate onto a GE Superdex 200 10/300 column at 20°C. 45 successive 1 second frames were collected through the SEC-elution sample peak. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.","tags":[],"intensity_unit":"arbitrary","experimental_mw":103.0,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":83.0,"porod_mw_error":null,"pddf_i0":82.07,"pddf_i0_error":null,"guinier_i0":80.97,"guinier_i0_error":0.22,"pddf_rg":3.96,"pddf_rg_error":null,"guinier_rg":3.78,"guinier_rg_error":0.05,"pddf_dmax":14.5,"pddf_dmax_error":null,"porod_volume":132.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":22,"guinier_point_last":124,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDFT8_datloglog_img.png","symmetry":null,"last_modified":"2023-06-21T07:56:39.492710+02:00","bragg_peak":[]}