{"code":"SASDXC4","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/SASDXC4.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDXC4.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXC4_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXC4_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDXC4_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDXC4_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDXC4.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 biogenesis factor 8","short_name":"Pex8","sequence":"GPMDMREAQRIPQQLDYLLAEIISPNEDTNVI\r\nGYLAYYYPKLKNEQNVALLTDFFLRCPTYFSHSNVVSLRNNYPVMEAFNYIMTTKFKVSQ\r\nPTVPFYRFYAAVLASLLNCEKTDPSHHWKLIPILTGVLLSIKGRDDVELYPDHSRSIKGS\r\nDTAVAQLLQRCLLRFYQSGDARSYDLNALVIISMSCALDYVEDDTIKKILYCFNYTRAII\r\nDLIYYSPYGLNDSDIPLLSDSSVNSQSFDQLLNNNPALKHLNRLSFLFERTVKLNDGSIQ\r\nSNLNDIDISLNKMQSFSEKLSKKISVLDDDSSKGVGQLLRQCLYASIIIHQAILTTFFQL\r\nDNADYTKYFLPSFSRKILSILFNLFFIVDRIGTGGFQPYNFVYLTCLQGIIQYDMKTAES\r\nLVKTFTTGINYSSLKDSEVARAKLLFTLNLMEQIVNICSDDLRLELIVPLVEDLVNNKNA\r\nCVDIHNHVFKSIFESAHSVILKFFTVVDSSVKNVDYETNVTLVSEKIIPYLTLVIDQFPE\r\nFLSINQLDIAIETISRTVFPDSPIYSYDKNISSMFLNVLFNKCLTVDNDELVELPAIEAV\r\nVAPKNDEENNTSDAQDGGPKELQSLNDLKSRRSALISALISVFPLIPVKDYTKWLSIAFY\r\nDLIVATPERTERAFLQERLWDCVVGTNKYDPQKGNLGIMWWYENVNAQSTAKL","organism":"Komagataella pastoris","uniprot_code":"Q01962","uniprot_range_first":33,"uniprot_range_last":713,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MYRLGSQGRSIQSQLQNGDSSSGRPLQLQGTGMREAQRIPQQLDYLLAEIISPNEDTNVI\nGYLAYYYPKLKNEQNVALLTDFFLRCPTYFSHSNVVSLRNNYPVMEAFNYIMTTKFKVSQ\nPTVPFYRFYAAVLASLLNCEKTDPSHHWKLIPILTGVLLSIKGRDDVELYPDHSRSIKGS\nDTAVAQLLQRCLLRFYQSGDARSYDLNALVIISMSCALDYVEDDTIKKILYCFNYTRAII\nDLIYYSPYGLNDSDIPLLSDSSVNSQSFDQLLNNNPALKHLNRLSFLFERTVKLNDGSIQ\nSNLNDIDISLNKMQSFSEKLSKKISVLDDDSSKGVGQLLRQCLYASIIIHQAILTTFFQL\nDNADYTKYFLPSFSRKILSILFNLFFIVDRIGTGGFQPYNFVYLTCLQGIIQYDMKTAES\nLVKTFTTGINYSSLKDSEVARAKLLFTLNLMEQIVNICSDDLRLELIVPLVEDLVNNKNA\nCVDIHNHVFKSIFESAHSVILKFFTVVDSSVKNVDYETNVTLVSEKIIPYLTLVIDQFPE\nFLSINQLDIAIETISRTVFPDSPIYSYDKNISSMFLNVLFNKCLTVDNDELVELPAIEAV\nVAPKNDEENNTSDAQDGGPKELQSLNDLKSRRSALISALISVFPLIPVKDYTKWLSIAFY\nDLIVATPERTERAFLQERLWDCVVGTNKYDPQKGNLGIMWWYENVNAQSTAKL","mw":78.017,"total_mw":78.017,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":"The protein construct used for SAXS contains an additional four non-native amino acids at the N-terminus (GPMD). The protein was expressed in E. coli BL21 DE3 Lobstr cells."},{"long_name":"Peroxisomal targeting signal receptor","short_name":"Pex5","sequence":"GPMDGRLNYGEYKYEEKNQFRNDPDAYEIGMRLMESGAKLSEAGLA \r\nFEAAVQQDPKHVDAWLKLGEVQTQNEKESDGIAALEKCLELDPTNLAALMTLAISYINDG \r\nYDNAAYATLERWIETKYPDIASRARSSNPDLDGGDRIEQNKRVTELFMKAAQLSPDVASM \r\nDADVQTGLGVLFYSMEEFDKTIDCFKAAIEVEPDKALNWNRLGAALANYNKPEEAVEAYS \r\nRALQLNPNFVRARYNLGVSFINMGRYKEAVEHLLTGISLHEVEGVDASEMSSNQGLQNNA \r\nLVETLKRAFLGMNRRDLVDKVYPGMGLAQFRKMFDF","organism":"Komagataella pastoris","uniprot_code":"P33292","uniprot_range_first":259,"uniprot_range_last":576,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MSLIGGGSDCAAGSNPLAQFTKHTQHDTSLQQSMRNGEFQQGNQRMMRNESTMSPMERQQ\nMDQFMQQQNNPAFNFQPMQHELNVMQQNMNAPQQVANNSWNQEFRMKDPMVANAPSAQVQ\nTPVQSTNWAQDFQQAGPEVQHHAQQHQHPILSVPGVRAGIYGGGRLMGGSMMNRAAQMQQ\nQNPAQAQTSEQSQTQWEDQFKDIESMLNSKTQEPKTKQQEQNTFEQVWDDIQVSYADVEL\nTNDQFQAQWEKDFAQYAEGRLNYGEYKYEEKNQFRNDPDAYEIGMRLMESGAKLSEAGLA\nFEAAVQQDPKHVDAWLKLGEVQTQNEKESDGIAALEKCLELDPTNLAALMTLAISYINDG\nYDNAAYATLERWIETKYPDIASRARSSNPDLDGGDRIEQNKRVTELFMKAAQLSPDVASM\nDADVQTGLGVLFYSMEEFDKTIDCFKAAIEVEPDKALNWNRLGAALANYNKPEEAVEAYS\nRALQLNPNFVRARYNLGVSFINMGRYKEAVEHLLTGISLHEVEGVDASEMSSNQGLQNNA\nLVETLKRAFLGMNRRDLVDKVYPGMGLAQFRKMFDF","mw":36.057,"total_mw":36.057,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":"The protein construct used for SAXS contains an additional four non-native amino acids at the N-terminus (GPMD). The protein was expressed and purified from E. coli Codon+ RIL."}],"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 biogenesis factor 8 (Pex8) bound to the C-terminal domain of Peroxisomal targeting signal receptor, Pex5 (Pex8-Pex5CTD complex 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":"2021-08-17","storage_temperature":10.0,"cell_temperature":20.0,"exposure_time":0.5,"number_of_frames":63,"wavelength":0.123982,"sample_detector_distance":3.0,"concentration_min":null,"concentration_max":5.8,"sample_volume":90.0,"flow_rate":0.6,"s_min":0.024,"s_max":7.395,"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/SASDXC4_fit1_model1.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/SASDXC4_fit1_model2_img.png","software":"SASREF","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDXC4_fit1_model2.pdb","model_mw":113.2,"bead_radius":null,"log":null,"symmetry":"P1","comment":"Individual SASREF model example (renumbered)","user":1019}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDXC4_fit1_fixed_fit_img.png","software":"CRYSOL","chi_square_value":1.093,"p_value":0.9067,"fit_residual_plot":"SASDXC4_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDXC4_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 using Bayesian inference in the MW rage of 92-107 kDa (datmw tool, ATSAS 3; GNOM.out file input). SASREF models and the unsubtracted SEC-SAXS data frames are made available in the full entry zip archive.","experiment_description":"Synchrotron SAXS data from solutions of the Pex8-Pex5CTD complex 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 storage ring (DESY; Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.123982 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 90.00 μl sample at 5.8 mg/ml was injected at a 0.60 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 20°C. 63 successive 0.500 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":101.0,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":88.0,"porod_mw_error":null,"pddf_i0":0.03591,"pddf_i0_error":null,"guinier_i0":0.0357463,"guinier_i0_error":null,"pddf_rg":4.311,"pddf_rg_error":null,"guinier_rg":4.211,"guinier_rg_error":0.01,"pddf_dmax":14.5,"pddf_dmax_error":null,"porod_volume":141.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":18,"guinier_point_last":103,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDXC4_datloglog_img.png","symmetry":null,"last_modified":"2025-09-03T12:12:42.430703+02:00","bragg_peak":[]}