{ "code": "SASDUV5", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/A", "project": { "title": "A Simple Protocol for Visualization of RNA-Protein Complexes by Atomic Force Microscopy.", "publication": { "title": "A Simple Protocol for Visualization of RNA-Protein Complexes by Atomic Force Microscopy.", "author_list": "Tripepi A, Shakoor H, Klapetek P", "journal": "Curr Protoc", "doi": "10.1002/cpz1.70084", "pmid": "39781608", "published_date": "2025 Jan" }, "status": "released", "submitted_date": "2024-03-22", "released_date": "2025-01-14" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDUV5.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDUV5.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUV5_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUV5_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDUV5_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUV5_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDUV5.sascif", "experiment": { "instrument": { "detector": { "type": "Hybrid Photon Counting (HPC) X-ray detector", "name": "Rigaku HyPix-3000", "resolution": 100.0 }, "name": "CEITEC", "city": "Brno", "country": "Czech Republic", "beamline_name": "Rigaku BioSAXS-2000", "beam_geometry": null, "type_of_source": "X-ray in house", "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": "3'UTR fragment of ADP-ribosylation factor 1", "short_name": "ARF1", "sequence": "GGAGUGCCAGAAGCUGCCUCUUCGGAGGCAGUUUCUGGUACUCC", "organism": "Homo sapiens", "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "RNA", "uniprot_sequence": "", "mw": 14.185, "total_mw": 14.185, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "" }, { "long_name": "Double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2 and truncated Staufen-swapping (ΔSSM)", "short_name": "Stau1dsRBD3endΔSSM", "sequence": "GSHMEENLNKSEISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSKKISKKNAAIAVLEELKKLPPLPAVERVKPRIEKKTKPIVKPQTSPEYGQGINPISRLAQIQQAKKEKEPEYTLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFKVPQAQPTKPALKSEEKTPIKKPGDGRKVTFFEPGSGDENGTSNKEDEFRMPYLSHQQLPAGILPMVPEVAQAVGVSQGHHTKDFTRAAPNPAKATVTAPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSELDQQSTEMPRTGNGPMSVCGRC", "organism": "Homo sapiens", "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MSQVQVQVQNPSAALSGSQILNKNQSLLSQPLMSIPSTTSSLPSENAGRPIQNSALPSAS\r\nITSTSAAAESITPTVELNALCMKLGKKPMYKPVDPYSRMQSTYNYNMRGGAYPPRYFYPF\r\nPVPPLLYQVELSVGGQQFNGKGKTRQAAKHDAAAKALRILQNEPLPERLEVNGRESEEEN\r\nLNKSEISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSKKISKKN\r\nAAIAVLEELKKLPPLPAVERVKPRIKKKTKPIVKPQTSPEYGQGINPISRLAQIQQAKKE\r\nKEPEYTLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFKVPQAQ\r\nPTKPALKSEEKTPIKKPGDGRKVTFFEPGSGDENGTSNKEDEFRMPYLSHQQLPAGILPM\r\nVPEVAQAVGVSQGHHTKDFTRAAPNPAKATVTAMIARELLYGGTSPTAETILKNNISSGH\r\nVPHGPLTRPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVES\r\nCHDMAALNILKLLSELDQQSTEMPRTGNGPMSVCGRC", "mw": 40.674, "total_mw": 81.348, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "The protein construct used for SAXS contains three additional non-native amino acids at the N-terminus (GSH)." } ], "buffer": { "name": "50 mM TRIS, 300 mM NaCl, 3.8 mM β-mercaptoethanol", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.0, "deuteration": null }, "purity_method": null, "name": "Human Double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2 and truncated Staufen-swapping (ΔSSM) motif bound to 3'UTR fragment of ADP-ribosylation factor 1", "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": "CEITEC - Central European Institute of Technology, Masaryk University", "webpage": "https://www.ceitec.eu/" } ], "contributor_name": "Tomas", "contributor_surname": "Klumpler", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2024-01-12", "storage_temperature": 4.0, "cell_temperature": 20.0, "exposure_time": 3600.0, "number_of_frames": 1, "wavelength": 0.154, "sample_detector_distance": 0.48, "concentration_min": null, "concentration_max": 3.2, "sample_volume": 100.0, "flow_rate": 0.6, "s_min": 0.1, "s_max": 4.007, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDUV5_fit1_model1_img.png", "software": "CORAL", "pdb_link": [], "model_title": null, "type_of_model": "mix", "software_version": "ATSAS 2.8.4 (r10552)", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDUV5_fit1_model1.pdb", "model_mw": 93.38, "bead_radius": 1.9, "log": null, "symmetry": null, "comment": null, "user": 195 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDUV5_fit1_fixed_fit_img.png", "software": "CORAL", "chi_square_value": 1.11, "p_value": 0.0549, "fit_residual_plot": "SASDUV5_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDUV5_fit1.fit", "fit_log": null, "software_version": "ATSAS 2.8.4 (r10552)", "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": null, "experiment_description": "SAXS data from solutions of double-stranded RNA-binding protein Staufen homolog 1 with truncated RNA-binding domain 2 and truncated Staufen-swapping (ΔSSM) motif bound to the 3'UTR fragment of ADP-ribosylation factor 1 in 50 mM TRIS, 300 mM NaCl, 3.8 mM β-mercaptoethanol, pH 7 were collected using a Rigaku BioSAXS-2000 instrument at CEITEC (Brno, Czech Republic) equipped with a Rigaku HyPix-3000 detector at a sample-detector distance of 0.5 m and at a wavelength of λ = 0.154 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.20 mg/ml was measured at 20°C. One 3600 second frame was 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": "arbitrary", "experimental_mw": 109.1, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 86.9, "porod_mw_error": null, "pddf_i0": 0.5567, "pddf_i0_error": null, "guinier_i0": 0.585799, "guinier_i0_error": null, "pddf_rg": 5.32, "pddf_rg_error": null, "guinier_rg": 5.471, "guinier_rg_error": 2.253, "pddf_dmax": 16.12, "pddf_dmax_error": null, "porod_volume": 139.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 17, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDUV5_datloglog_img.png", "symmetry": null, "last_modified": "2025-01-14T14:00:42.833878+01:00", "bragg_peak": [] }