The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
Every source field is expanded here, including empty values, list members and fields already shown above.
View the complete summary.json source
{
"code": "SASDVQ6",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Selective cargo and membrane recognition by SNX17 regulates its interaction with Retriever",
"publication": {
"title": "Selective cargo and membrane recognition by SNX17 regulates its interaction with Retriever",
"author_list": "Martín-González A, Méndez-Guzmán I, Zabala-Zearreta M, Quintanilla A, García-López A, Martínez-Lombardía E, Albesa-Jové D, Acosta J, Lucas M",
"journal": "EMBO Reports",
"doi": "10.1038/s44319-024-00340-1",
"pmid": null,
"published_date": "2024 Dec 09"
},
"status": "released",
"submitted_date": "2024-08-27",
"released_date": "2024-11-21"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDVQ6.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVQ6.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVQ6_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVQ6_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVQ6_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVQ6_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVQ6.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Eiger 4M",
"resolution": 75.0
},
"name": "Diamond Light Source",
"city": "Didcot",
"country": "UK",
"beamline_name": "B21",
"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": "VPS35 endosomal protein-sorting factor-like",
"short_name": "VPS35L",
"sequence": "GMAVFPWHSRNRNYKAEFASCRLEAVPLEFGDYHPLKPITVTESKTKKVNRKGSTSSTSSSSSSSVVDPLSSVLDGTDPLSMFAATADPAALAAAMDSSRRKRDRDDNSVVGSDFEPWTNKRGEILARYTTTEKLSINLFMGSEKGKAGTATLAMSEKVRTRLEELDDFEEGSQKELLNLTQQDYVNRIEELNQSLKDAWASDQKVKALKIVIQCSKLLSDTSVIQFYPSKFVLITDILDTFGKLVYERIFSMCVDSRSVLPDHFSPENANDTAKETCLNWFFKIASIRELIPRFYVEASILKCNKFLSKTGISECLPRLTCMIRGIGDPLVSVYARAYLCRVGMEVAPHLKETLNKNFFDFLLTFKQIHGDTVQNQLVVQGVELPSYLPLYPPAMDWIFQCISYHAPEALLTEMMERCKKLGNNALLLNSVMSAFRAEFIATRSMDFIGMIKECDESGFPKHLLFRSLGLNLALADPPESDRLQILNEAWKVITKLKNPQDYINCAEVWVEYTCKHFTKREVNTVLADVIKHMTPDRAFEDSYPQLQLIIKKVIAHFHDFSVLFSVEKFLPFLDMFQKESVRVEVCKCIMDAFIKHQQEPTKDPVILNALLHVCKTMHDSVNALTLEDEKRMLSYLINGFIKMVSFGRDFEQQLSFYVESRSMFCNLEPVLVQLIHSVNRLAMETRKVMKGNHSRKTAAFVRACVAYCFITIPSLAGIFTRLNLYLHSGQVALANQCLSQADAFFKAAISLVPEVPKMINIDGKMRPSESFLLEFLCNFFSTLLIVPDHPEHGVLFLVRELLNVIQDYTWEDNSDEKIRIYTCVLHLLSAMSQETYLYHIDKVDSNDSLYGGDSKFLAENNKLCETVMAQILEHLKTLAKDEALKRQSSLGLSFFNSILAHGDLRNNKLNQLSVNLWHLAQRHGCADTRTMVKTLEYIKKQSKQPDMTHLTELALRLPLQTRT",
"organism": "Homo sapiens",
"uniprot_code": "Q7Z3J2",
"uniprot_range_first": 1,
"uniprot_range_last": 963,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MAVFPWHSRNRNYKAEFASCRLEAVPLEFGDYHPLKPITVTESKTKKVNRKGSTSSTSSS\nSSSSVVDPLSSVLDGTDPLSMFAATADPAALAAAMDSSRRKRDRDDNSVVGSDFEPWTNK\nRGEILARYTTTEKLSINLFMGSEKGKAGTATLAMSEKVRTRLEELDDFEEGSQKELLNLT\nQQDYVNRIEELNQSLKDAWASDQKVKALKIVIQCSKLLSDTSVIQFYPSKFVLITDILDT\nFGKLVYERIFSMCVDSRSVLPDHFSPENANDTAKETCLNWFFKIASIRELIPRFYVEASI\nLKCNKFLSKTGISECLPRLTCMIRGIGDPLVSVYARAYLCRVGMEVAPHLKETLNKNFFD\nFLLTFKQIHGDTVQNQLVVQGVELPSYLPLYPPAMDWIFQCISYHAPEALLTEMMERCKK\nLGNNALLLNSVMSAFRAEFIATRSMDFIGMIKECDESGFPKHLLFRSLGLNLALADPPES\nDRLQILNEAWKVITKLKNPQDYINCAEVWVEYTCKHFTKREVNTVLADVIKHMTPDRAFE\nDSYPQLQLIIKKVIAHFHDFSVLFSVEKFLPFLDMFQKESVRVEVCKCIMDAFIKHQQEP\nTKDPVILNALLHVCKTMHDSVNALTLEDEKRMLSYLINGFIKMVSFGRDFEQQLSFYVES\nRSMFCNLEPVLVQLIHSVNRLAMETRKVMKGNHSRKTAAFVRACVAYCFITIPSLAGIFT\nRLNLYLHSGQVALANQCLSQADAFFKAAISLVPEVPKMINIDGKMRPSESFLLEFLCNFF\nSTLLIVPDHPEHGVLFLVRELLNVIQDYTWEDNSDEKIRIYTCVLHLLSAMSQETYLYHI\nDKVDSNDSLYGGDSKFLAENNKLCETVMAQILEHLKTLAKDEALKRQSSLGLSFFNSILA\nHGDLRNNKLNQLSVNLWHLAQRHGCADTRTMVKTLEYIKKQSKQPDMTHLTELALRLPLQ\nTRT",
"mw": 109.618,
"total_mw": 109.618,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "Subunit of the Retriever complex with an extra G at the N-terminus."
},
{
"long_name": "Vacuolar protein sorting-associated protein 29",
"short_name": "VPS29",
"sequence": "MLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHKFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYKKP",
"organism": "Homo sapiens",
"uniprot_code": "Q9UBQ0",
"uniprot_range_first": 1,
"uniprot_range_last": 182,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVR\nGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHKFE\nAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYK\nKP",
"mw": 20.505,
"total_mw": 20.505,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "Subunit of the Retriever complex."
},
{
"long_name": "Vacuolar protein sorting-associated protein 26C",
"short_name": "VPS26C",
"sequence": "GMGTALDIKIKRANKVYHAGEVLSGVVVISSKDSVQHQGVSLTMEGTVNLQLSAKSVGVFEAFYNSVKPIQIINSTIEMVKPGKFPSGKTEIPFEFPLHLKGNKVLYETYHGVFVNIQYTLRCDMKRSLLAKDLTKTCEFIVHSAPQKGKFTPSPVDFTITPETLQNVKERALLPKFLLRGHLNSTNCVITQPLTGELVVESSEAAIRSVELQLVRVETCGCAEGYARDATEIQNIQIADGDVCRGLSVPIYMVFPRLFTCPTLETTNFKVEFEVNIVVLLHPDHLITENFPLKLCRI",
"organism": "Homo sapiens",
"uniprot_code": "O14972",
"uniprot_range_first": 1,
"uniprot_range_last": 297,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MGTALDIKIKRANKVYHAGEVLSGVVVISSKDSVQHQGVSLTMEGTVNLQLSAKSVGVFE\nAFYNSVKPIQIINSTIEMVKPGKFPSGKTEIPFEFPLHLKGNKVLYETYHGVFVNIQYTL\nRCDMKRSLLAKDLTKTCEFIVHSAPQKGKFTPSPVDFTITPETLQNVKERALLPKFLLRG\nHLNSTNCVITQPLTGELVVESSEAAIRSVELQLVRVETCGCAEGYARDATEIQNIQIADG\nDVCRGLSVPIYMVFPRLFTCPTLETTNFKVEFEVNIVVLLHPDHLITENFPLKLCRI",
"mw": 33.067,
"total_mw": 33.067,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "Subunit of the Retriever complex with an extra G at the N-terminus."
}
],
"buffer": {
"name": "50 mM Tris, 200 mM NaCl, 1 mM TCEP",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Retriever complex",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": null,
"full_name": "Universidad de Cantabria",
"webpage": null
}
],
"contributor_name": "María",
"contributor_surname": "Lucas",
"orcid": "http://orcid.org/0000-0002-7854-4249"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2022-04-28",
"storage_temperature": -80.0,
"cell_temperature": 15.0,
"exposure_time": 3.0,
"number_of_frames": 600,
"wavelength": 0.0954,
"sample_detector_distance": 3.688,
"concentration_min": null,
"concentration_max": 5.0,
"sample_volume": 45.0,
"flow_rate": 0.16,
"s_min": 0.045,
"s_max": 3.4,
"total_exposure_time": null,
"seccolumn": 19
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVQ6_fit1_model1_img.png",
"software": "AlphaFold",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "Multimer",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDVQ6_fit1_model1.pdb",
"model_mw": 163.0,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 1116
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVQ6_fit1_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.502,
"p_value": 0.0,
"fit_residual_plot": null,
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVQ6_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Retriever_ma-3cag5.log",
"software_version": "2.8.3",
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVQ6_fit2_model1_img.png",
"software": "AlphaFold",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "Multimer",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDVQ6_fit2_model1.pdb",
"model_mw": 163.0,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "Cryo-EM structure (pdbID:8SYN) was used as template in AlphaFold Multimer to model the missing loops",
"user": 1116
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVQ6_fit2_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.515,
"p_value": 0.0,
"fit_residual_plot": null,
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVQ6_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Retriever_8SYN.log",
"software_version": "2.8.3",
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVQ6_fit3_model1_img.png",
"software": "GASBOR",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "2.3i",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDVQ6_fit3_model1.pdb",
"model_mw": null,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 1116
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVQ6_fit3_fixed_fit_img.png",
"software": "GASBOR",
"chi_square_value": 1.23,
"p_value": 0.0,
"fit_residual_plot": "SASDVQ6_fit3_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVQ6_fit3.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Retriever_GASBOR.log",
"software_version": "2.3i",
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of the Retriever complex in 50 mM Tris, 200 mM NaCl, 1 mM TCEP, pH 7.5 were collected on the B21 beam line at the Diamond Light Source (Didcot, UK) using a Eiger 4M detector at a sample-detector distance of 3.7 m and at a wavelength of λ = 0.0954 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 45.00 μl sample at 5 mg/ml was injected at a 0.16 ml/min flow rate onto a Shodex KW403-4F column at 15°C. 600 successive 3 second frames were collected. 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": "arbitrary",
"experimental_mw": 169.83,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 160.0,
"porod_mw_error": null,
"pddf_i0": 0.1292,
"pddf_i0_error": null,
"guinier_i0": 0.128425,
"guinier_i0_error": null,
"pddf_rg": 5.35,
"pddf_rg_error": null,
"guinier_rg": 5.207,
"guinier_rg_error": 0.114,
"pddf_dmax": 21.5,
"pddf_dmax_error": null,
"porod_volume": 256.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 7,
"guinier_point_last": 154,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDVQ6_datloglog_img.png",
"symmetry": null,
"last_modified": "2024-12-09T22:45:42.329161+01:00",
"bragg_peak": []
}
