{ "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": [] }