{ "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": [] }