{ "code": "SASDUY7", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/nm", "project": { "title": "Structural and functional repurposing of picornaviral H-box 2A proteins", "publication": null, "status": "released", "submitted_date": "2024-04-30", "released_date": "2026-04-30" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDUY7.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDUY7.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUY7_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUY7_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDUY7_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUY7_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDUY7.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": "Genome polyprotein", "short_name": "AiV-2A", "sequence": "GPGGAASATPDVDPDDRVYIVRAQRPTYVHWAIRKVAPDGSAKQISLSRSGIQALVALEPPEGEPYLEILPSHWTLAELQLGNKWEYSATNNCTHFVSSITGESLPNTGFSLALGIGALTAIAASAAVAVKALPGIRRQ", "organism": "Aichi virus (strain Human/A846/88/1989)", "uniprot_code": "O91464", "uniprot_range_first": 1017, "uniprot_range_last": 1152, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MAATRVSRSVLAAVAHSAAHRTYHTVLDCYDRLYLNTNPHLSYPLPKNSSFPCPFCQYDE\nQNEVLSPESLRGEGAEPCWKCSQDKPRRKYNTTPPEDWLYDSDVQSWFYPETYYSDLQQK\nFFDKLALLSLPGAYQAKTPEERALAGALTQLLNFPSTPPLTLPTTNLQRQGNSVTNIYGN\nGNNVTTDVGANGWAPTVSTGLGDGPVSASADSLPGRSGGASSEKTHTVSGSSNKVGSRFS\nKWWEPAAARASESATDSAIEGIDAAGKAASKAITRKLDRPAAPSSTANPQPSLIALNPSA\nTQSGNASILTGSTAPSLLAYPTATPVPLPNPDEPSQPGPSGDRTWLLDTVTWSQEFTRGW\nNIAGSNGMQWTGLESLIFPVSTDTNWTSTSSPTAYPLPFSFVRAYPDSSWAAMYNTHSMW\nNCGWRVQVTVNGSQFHAGALILYMVPEATTHAIQTARDNAGFVFPYVILNLYESNTATIE\nVPYISPTPNTSSGLHAPWTFYLQVLSPLNPPPSLPTSLSCSIYVTPVDSSFHGLRYLAPQ\nHWKTRAVPGAGTFGSAVAGQELPLCGVRAYYPPNAYIPAQVRDWLEFAHRPGLMATVPWT\nMADEPAERLGIFPVSPSAIAGTGAPISYVISLFSQWRGELAAHLLFTGSAQHYGRLVVCY\nTPAAPQPPSTMQEAMRGTYTVWDVNAASTLEFTIPFISNSYWKTVDVNNPDALLSTTGYV\nSIWVQNPLVGPHTAPASALVQAFISAGESFNVRLMQNPALTSQTLTEDLDAPQDTGNIEN\nGAADNSPQPRTTFDYTGNPLPPDTKLENFFSFYRLLPMGGSGAPSLSFPADEGTIIPLNP\nINWLKGADVSGIAAMLSCFTYIAADLRITLRFSNPNDNPATMLVAFAPPGATIPLKPTRQ\nMLSNFYMAEVPVSAATSTMVSFSIPYTSPLSAIPTSYFGWEDWSGTNFGQLSSGSWGNLM\nLIPSLSVDSAIPFDFQLSCWVAFGNFKAWVPRPPPPLPPLPTPAANAERTVAVIKQGAAS\nATPDVDPDDRVYIVRAQRPTYVHWAIRKVAPDGSAKQISLSRSGIQALVALEPPEGEPYL\nEILPSHWTLAELQLGNKWEYSATNNCTHFVSSITGESLPNTGFSLALGIGALTAIAASAA\nVAVKALPGIRRQGLLTLSADTETNQTLNKITESVNQAAQVVSQFDLSGPANSVSLAASDI\nREAAHKVASSLNGFTDVIADIKDSLFTRVSDAVESGVATFLTWLVKLFGYLLVLFGSPTP\nMSISGLLVIICADLAPHAREFFTASGNVLSSLYYWIASKLGLSVTPQECERATLEPQGLK\nDFNDGALAMRNVEWIGETAWKWAHRLLDWIRGKAKTDPQAKLADVHDEIMLHYSDSILAL\nGSEKLPIDHITKSISRCRELVSIAQEAKSGPHSSFLNQAIKNYTLAISQHRKCQTGPRPE\nPVVVYLYGPPGTGKSLLASLLAQTLSQRLAGTPDDVYSPSSASCEYFDGYTGQTVHFIDD\nIGQDPEGRDWANFPNLVSSAPFIVPMASLEEKGTHYTSKVIVVTSNFHEPNERAARSMGA\nLRRRVHLRINVTSNGVPFDPTNALNPIPGTQSKYFTAQTPLTLFQSNTVRLDRDSIWTPT\nFTNMDELVDAIVTRLDRSTGVSNSLASLIRRQGNRVIDAEPREIPLEYADDLLEAMAHHR\nPVPCSLGLSQAIANNTPIQQISETFWKYRKPIFTCTTFLAVLGFLCSVIPLARSLWKSKQ\nDTPQEPQAAYSAISHQKPKPKSQKPVPTRHIQRQGISPAVPGISNNVVHVESGNGLNKNV\nMSGFYIFSRFLLVPTHLREPHHTTLTVGADTYDWATLQTQEFGEITIVHTPTSRQYKDMR\nRFIGAHPHPTGLLVSQFKAAPLYVRISDNRILDLDFPGVVVCKQAYGYRAATFEGLCGSP\nLVTDDPSGVKILGLHVAGVAGTSGFSAPIHPILGQITQFATTQQSLIVPTAEVRPGVNVN\nRMSRLHPSPAYGAFPVKKQPAPLKRNDKRLQEGVDLDTQLFLKHGKGDVTEPWPGLEAAA\nDLYFSTFPTSLPVLTQEQAIHGTPNMEGLDMGQAAGYPWNTLGRSRRSLFDEVEPGVFVP\nKPELQAEINQTLEDPDYVYSTFLKDELRPTAKVEQGLTRIVEAAPIHAIVAGRMLLGGLI\nDYMQGRPGEHGSAVGCNPDVHWTSFFYAFSEFSQVYDLDYKCFDATLPSAVFTLVADHLT\nRITGDPRVGRYIHSIRHSHHIYGNRMYDMIGGNPSGCVATSILNTIINNICVLSALIQHP\nDFSPSRFHILAYGDDVIYATEPPIHPSFLREFYQKHTPLVVTPANKGQDFPPTSTIYEVT\nFLKRWFVPDDVRPIYIHPVMDPDTYEQSVMWLRDGDFQDVVTSLCHLAFHSGPKTYAAWC\nMKVREQCLKSGFAPNFLPYSYLQLRWLNLLAA", "mw": 14.63, "total_mw": 14.63, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "Aichivirus 2A protein from the Genome polyprotein. Recombinant protein expressed in E.coli." } ], "buffer": { "name": "20 mM HEPES,150 mM NaCl, 2 mM TCEP, 1% v/v glycerol", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.4, "deuteration": null }, "purity_method": null, "name": "Aichivirus A 2A protein at neutral pH", "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": "Linköping University ", "webpage": null } ], "contributor_name": "Marion", "contributor_surname": "Pichon", "orcid": "https://orcid.org/0000-0002-8511-4298" } ], "concentration_method": null, "concentration_unit": null, "date": "2022-03-11", "storage_temperature": 10.0, "cell_temperature": 20.0, "exposure_time": 0.24, "number_of_frames": 2880, "wavelength": 0.1549, "sample_detector_distance": 4.0, "concentration_min": null, "concentration_max": 10.0, "sample_volume": 40.0, "flow_rate": 0.35, "s_min": 0.013, "s_max": 4.445, "total_exposure_time": null, "seccolumn": 4 }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDUY7_fit1_model1_img.png", "software": "PyMOL", "pdb_link": [ { "pdb_code": "7zv6", "ext_code": "7ZV6", "ext_type": "pdb", "difference_with_model": "identical" } ], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDUY7_fit1_model1.pdb", "model_mw": 37.0, "bead_radius": null, "log": "https://www.sasbdb.org/media/log_files/7ZV6.log", "symmetry": null, "comment": "Chains A+B+C used as model for rigid body analysis", "user": 990 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDUY7_fit1_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 153.4922, "p_value": 0.0, "fit_residual_plot": "SASDUY7_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDUY7_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/7ZV6_chromixs66cut.log", "software_version": "crysol, ATSAS 3.2.1 (r14885)", "description": "Rigid body fit of the chains A + B + C" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDUY7_fit2_model1_img.png", "software": "PyMOL", "pdb_link": [ { "pdb_code": "7zv6", "ext_code": "7ZV6", "ext_type": "pdb", "difference_with_model": "identical" } ], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDUY7_fit2_model1.pdb", "model_mw": 12.82, "bead_radius": null, "log": null, "symmetry": null, "comment": "Chains B used for model fitting.", "user": 990 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDUY7_fit2_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 10.96, "p_value": 0.0, "fit_residual_plot": "SASDUY7_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDUY7_fit2.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/7ZV6_B_chromixs66cut.log", "software_version": "crysol, ATSAS 3.2.1 (r14885)", "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDUY7_fit3_model1_img.png", "software": "SREFLEX", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": "sreflex, ATSAS 3.2.1 (r14885)", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDUY7_fit3_model1.pdb", "model_mw": 12.82, "bead_radius": null, "log": null, "symmetry": null, "comment": "Model obtained from sReflex with 7ZV6 Chain B as template", "user": 990 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDUY7_fit3_fixed_fit_img.png", "software": "SREFLEX", "chi_square_value": 5.09, "p_value": 0.0, "fit_residual_plot": "SASDUY7_fit3_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDUY7_fit3.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": "Data were processed using the ATSAS suite. The high resolution structure of AiV-2A (chain A, B, C and A+B+C) theoretical scattering curve was fitted to the experimental data using rigid body and normal mode analysis (SREFLEX). CAUTION: The monomer component of the models (12.8 kDa) does not include all of the amino acids of the protein construct used for SAXS (14.6 kDa).", "experiment_description": "Synchrotron SAXS data from solutions of Aichivirus A 2A protein at neutral pH in 20 mM HEPES,150 mM NaCl, 2 mM TCEP, 1% v/v glycerol, pH 7.4 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 4 m and at a wavelength of λ = 0.1549 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 40.00 μl sample at 10 mg/ml was injected at a 0.35 ml/min flow rate onto a GE Superdex 75 Increase 5/150 column at 20°C. 2880 successive 0.240 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": "1/cm", "experimental_mw": 12.025, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 10.98, "porod_mw_error": null, "pddf_i0": 0.03016, "pddf_i0_error": 3.526e-05, "guinier_i0": 0.0299389, "guinier_i0_error": null, "pddf_rg": 1.863, "pddf_rg_error": 0.005, "guinier_rg": 1.785, "guinier_rg_error": 0.006, "pddf_dmax": 7.4, "pddf_dmax_error": null, "porod_volume": 17.57, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 52, "guinier_point_last": 426, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDUY7_datloglog_img.png", "symmetry": null, "last_modified": "2026-04-30T16:35:52.435483+02:00", "bragg_peak": [] }