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{
"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": []
}
