{"code":"SASDX84","status":"Published","type_of_curve":"SEC-SAS","angular_unit":"1/nm","project":{"title":"Structure of Pex8 in complex with peroxisomal receptor Pex5 reveals its essential role in peroxisomal cargo translocation","publication":{"title":"Structure of Pex8 in complex with peroxisomal receptor Pex5 reveals its essential role in peroxisomal cargo translocation","author_list":"Ekal L, Wendscheck D, David Y, Chojnowski G, Jeffries C, Mullapudi E, Schuldiner M, Warscheid B, Zalckvar E, Wilmanns M","journal":null,"doi":"10.1101/2025.08.30.673231","pmid":null,"published_date":"2025 Sep 02"},"status":"released","submitted_date":"2025-04-25","released_date":"2025-09-03"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDX84.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDX84.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX84_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX84_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDX84_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX84_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDX84.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":"Peroxisomal targeting signal receptor","short_name":"Pex5","sequence":"GAMSLIGGGSDCAAGSNPLAQFTKHTQHDTSLQQSMRNGEFQQGNQRMMRNESTMSPMERQQ MDQFMQQQNNPAFNFQPMQHELNVMQQNMNAPQQVANNSWNQEFRMKDPMVANAPSAQVQ TPVQSTNWAQDFQQAGPEVQHHAQQHQHPILSVPGVRAGIYGGGRLMGGSMMNRAAQMQQ QNPAQAQTSEQSQTQWEDQFKDIESMLNSKTQEPKTKQQEQNTFEQVWDDIQVSYADVEL TNDQFQAQWEKDFAQYAEGRLNYGEYKYEEKNQFRNDPDAYEIGMRLMESGAKLSEAGLA FEAAVQQDPKHVDAWLKLGEVQTQNEKESDGIAALEKCLELDPTNLAALMTLAISYINDG YDNAAYATLERWIETKYPDIASRARSSNPDLDGGDRIEQNKRVTELFMKAAQLSPDVASM DADVQTGLGVLFYSMEEFDKTIDCFKAAIEVEPDKALNWNRLGAALANYNKPEEAVEAYS RALQLNPNFVRARYNLGVSFINMGRYKEAVEHLLTGISLHEVEGVDASEMSSNQGLQNNA\r\nLVETLKRAFLGMNRRDLVDKVYPGMGLAQFRKMFDF","organism":"Komagataella pastoris","uniprot_code":"P33292","uniprot_range_first":1,"uniprot_range_last":576,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MSLIGGGSDCAAGSNPLAQFTKHTQHDTSLQQSMRNGEFQQGNQRMMRNESTMSPMERQQ\nMDQFMQQQNNPAFNFQPMQHELNVMQQNMNAPQQVANNSWNQEFRMKDPMVANAPSAQVQ\nTPVQSTNWAQDFQQAGPEVQHHAQQHQHPILSVPGVRAGIYGGGRLMGGSMMNRAAQMQQ\nQNPAQAQTSEQSQTQWEDQFKDIESMLNSKTQEPKTKQQEQNTFEQVWDDIQVSYADVEL\nTNDQFQAQWEKDFAQYAEGRLNYGEYKYEEKNQFRNDPDAYEIGMRLMESGAKLSEAGLA\nFEAAVQQDPKHVDAWLKLGEVQTQNEKESDGIAALEKCLELDPTNLAALMTLAISYINDG\nYDNAAYATLERWIETKYPDIASRARSSNPDLDGGDRIEQNKRVTELFMKAAQLSPDVASM\nDADVQTGLGVLFYSMEEFDKTIDCFKAAIEVEPDKALNWNRLGAALANYNKPEEAVEAYS\nRALQLNPNFVRARYNLGVSFINMGRYKEAVEHLLTGISLHEVEGVDASEMSSNQGLQNNA\nLVETLKRAFLGMNRRDLVDKVYPGMGLAQFRKMFDF","mw":65.211,"total_mw":65.211,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":"The protein construct used for SAXS contains an additional two non-native amino acids at the N-terminus (GA). The protein was expressed in E. coli Codon+ RIL cells."}],"buffer":{"name":"50 mM HEPES, 150 mM NaCl, 3% v/v glycerol","concentration_unit":null,"comment":"0.2um filtered and degassed","additive":null,"concentration":null,"pka":null,"ph":7.5,"deuteration":null},"purity_method":null,"name":"Peroxisomal targeting signal receptor Pex5 from P. pastoris","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":"Lakhan","contributor_surname":"Ekal","orcid":"https://orcid.org/0000-0001-8916-4201"}],"concentration_method":null,"concentration_unit":null,"date":"2020-05-15","storage_temperature":10.0,"cell_temperature":20.0,"exposure_time":1.0,"number_of_frames":59,"wavelength":0.124026,"sample_detector_distance":3.0,"concentration_min":null,"concentration_max":8.0,"sample_volume":77.0,"flow_rate":0.65,"s_min":0.03,"s_max":7.265,"total_exposure_time":null,"seccolumn":1},"fits":[{"models":[{"model_plot":null,"software":"Other [static image]","pdb_link":[],"model_title":null,"type_of_model":"other","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDX84_fit1_model1.png","model_mw":null,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":1019},{"model_plot":null,"software":"Other [static image]","pdb_link":[],"model_title":null,"type_of_model":"other","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDX84_fit1_model2.png","model_mw":null,"bead_radius":null,"log":null,"symmetry":null,"comment":null,"user":1019},{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDX84_fit1_model3_img.png","software":"MultiFoXS","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDX84_fit1_model3.pdb","model_mw":65.18,"bead_radius":1.9,"log":null,"symmetry":null,"comment":null,"user":1019}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDX84_fit1_fixed_fit_img.png","software":"OLIGOMER","chi_square_value":1.02,"p_value":0.4865,"fit_residual_plot":"SASDX84_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDX84_fit1.fit","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":"The experimental molecular weight was estimated from combined multi-angle laser light scattering (MALLS) and refractive index (RI) measurements. These MALLS/RI data, in addition to the unsubtracted SEC-SAXS data frames, MultiFoXS ensemble modelling, and final OLIGOMER volume-fraction weighted fit are made available in the full entry zip archive. The models displayed in this entry represent the volume-fraction weighted ensemble of Pex5 (top), the Rg frequency of each model in the limited ensemble 9-member pool (middle), and an individual model example (most frequent representative, Vf = 0.45).","experiment_description":"Synchrotron SAXS data from solutions of Pex5 in 50 mM HEPES, 150 mM NaCl, 3% v/v glycerol, pH 7.5 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 = 0.124026 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 77.00 μl sample at 8 mg/ml was injected at a 0.65 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 20°C. 59 successive 1 second frames were collected through the main SEC elution 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":"1/cm","experimental_mw":68.1,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":81.0,"porod_mw_error":null,"pddf_i0":2377.0,"pddf_i0_error":null,"guinier_i0":2351.1,"guinier_i0_error":null,"pddf_rg":5.365,"pddf_rg_error":null,"guinier_rg":5.035,"guinier_rg_error":0.021,"pddf_dmax":21.4,"pddf_dmax_error":null,"porod_volume":131.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":11,"guinier_point_last":70,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDX84_datloglog_img.png","symmetry":null,"last_modified":"2025-09-03T12:12:24.578381+02:00","bragg_peak":[]}