{"code":"SASDV56","status":"Published","type_of_curve":"Single concentration","angular_unit":"1/nm","project":{"title":"Conformational signatures induced by ubiquitin modification in the amyloid-forming tau repeat domain.","publication":{"title":"Conformational signatures induced by ubiquitin modification in the amyloid-forming tau repeat domain.","author_list":"Viola G, Trivellato D, Laitaoja M, Jänis J, Felli IC, D'Onofrio M, Mollica L, Giachin G, Assfalg M","journal":"Proc Natl Acad Sci U S A","doi":"10.1073/pnas.2425831122","pmid":"40198698","published_date":"2025 Apr 15"},"status":"released","submitted_date":"2024-08-13","released_date":"2025-03-21"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDV56.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDV56.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDV56_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDV56_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDV56_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDV56_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDV56.sascif","experiment":{"instrument":{"detector":{"type":null,"name":"Pilatus 6M","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":"Isoform Tau-F of Microtubule-associated protein tau (C291A, K311C, K317C, C322A)","short_name":"tau4RD domain","sequence":"MQTAPVPMPDLKNVKSKIGSTENLKHQPGGGKVQIINKKLDLSNVQSKAGSKDNIKHV\r\nPGGGSVQIVYCPVDLSCVTSKAGSLGNIHHKPGGGQVEVKSEKLDFKDRVQSKIGSLDNITHVPGGGNKKIE","organism":"Homo sapiens","uniprot_code":"P10636","uniprot_range_first":244,"uniprot_range_last":372,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MAEPRQEFEVMEDHAGTYGLGDRKDQGGYTMHQDQEGDTDAGLKESPLQTPTEDGSEEPG\nSETSDAKSTPTAEDVTAPLVDEGAPGKQAAAQPHTEIPEGTTAEEAGIGDTPSLEDEAAG\nHVTQARMVSKSKDGTGSDDKKAKGADGKTKIATPRGAAPPGQKGQANATRIPAKTPPAPK\nTPPSSGEPPKSGDRSGYSSPGSPGTPGSRSRTPSLPTPPTREPKKVAVVRTPPKSPSSAK\nSRLQTAPVPMPDLKNVKSKIGSTENLKHQPGGGKVQIINKKLDLSNVQSKCGSKDNIKHV\nPGGGSVQIVYKPVDLSKVTSKCGSLGNIHHKPGGGQVEVKSEKLDFKDRVQSKIGSLDNI\nTHVPGGGNKKIETHKLTFRENAKAKTDHGAEIVYKSPVVSGDTSPRHLSNVSSTGSIDMV\nDSPQLATLADEVSASLAKQGL","mw":13.7,"total_mw":13.7,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":"Tau4RD (Q244-E372 plus initial methionine) with C291A, C322A, K311C, K317C mutations referred to as tau4RDΔC(311/317C)"},{"long_name":"Polyubiquitin-B","short_name":null,"sequence":"MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPP\r\nDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGC","organism":"Fukomys damarensis","uniprot_code":"A0A091E260","uniprot_range_first":1,"uniprot_range_last":77,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN\nIQKESTLHLVLRLRGGC","mw":8.668,"total_mw":8.668,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":"The semisynthetic ubiquitination reaction was performed without major modifications to the already outlined protocol. Briefly, Ub-SH was activated with 5,5′-dithiobis(2-nitrobenzoic acid) (DTNB) and incubated with each tau mutant in a 1:4 tau:Ub molar ratio. The desired proteoform was then purified through ion exchange chromatography exploiting a linear gradient of NaCl."}],"buffer":{"name":"100 mM NaCl","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":6.8,"deuteration":null},"purity_method":null,"name":"Microtubule-associated protein tau, lysine-rich four-repeat domain 4RD synthetically linked to Ubiquitin at tau residue C317","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":"ESRF","address":"Grenoble, France","full_name":"European Synchrotron Radiation Facility","webpage":"http://www.esrf.eu/"}],"contributor_name":"Gabriele","contributor_surname":"Giachin","orcid":"https://orcid.org/0000-0001-7550-0307"}],"concentration_method":null,"concentration_unit":null,"date":"2023-03-17","storage_temperature":10.0,"cell_temperature":20.0,"exposure_time":0.05,"number_of_frames":20,"wavelength":0.123972,"sample_detector_distance":3.0,"concentration_min":null,"concentration_max":3.0,"sample_volume":null,"flow_rate":null,"s_min":0.09,"s_max":3.998,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDV56_fit1_model1_img.png","software":"EOM/RANCH","pdb_link":[],"model_title":null,"type_of_model":"mix","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDV56_fit1_model1.pdb","model_mw":10.58,"bead_radius":1.9,"log":null,"symmetry":null,"comment":null,"user":388}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDV56_fit1_fixed_fit_img.png","software":"EOM/GAJOE","chi_square_value":1.045,"p_value":0.28,"fit_residual_plot":"SASDV56_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDV56_fit1.fit","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/logFile_001_1_tVYO25T.log","software_version":null,"description":""},{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDV56_fit2_model1_img.png","software":"AMBER","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDV56_fit2_model1.pdb","model_mw":22.3,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":9}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDV56_fit2_fixed_fit_img.png","software":"CRYSOL","chi_square_value":1.272,"p_value":0.0013,"fit_residual_plot":"SASDV56_fit2_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDV56_fit2.fit","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/crysol_summary_LdowpMg.txt","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":"Synchrotron SAXS data from solutions of microtubule-associated protein tau (lysine-rich four-repeat domain 4RD) synthetically linked to ubiquitin at tau amino acid C317 in 100 mM NaCl, pH 6.8 were collected on the EMBL P12 beam line at PETRA III (DESY; Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.123972 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.00 mg/ml was measured at 20°C. 20 successive 0.050 second frames were collected. 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":"1/cm","experimental_mw":20.66,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":25.8,"porod_mw_error":null,"pddf_i0":0.0499,"pddf_i0_error":null,"guinier_i0":0.0489423,"guinier_i0_error":null,"pddf_rg":3.598,"pddf_rg_error":null,"guinier_rg":3.34,"guinier_rg_error":0.046,"pddf_dmax":13.3,"pddf_dmax_error":null,"porod_volume":41.3,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":12,"guinier_point_last":104,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDV56_datloglog_img.png","symmetry":null,"last_modified":"2025-04-10T13:15:30.028980+02:00","bragg_peak":[]}