{"code":"SASDUZ7","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/SASDUZ7.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDUZ7.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUZ7_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUZ7_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDUZ7_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDUZ7_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDUZ7.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 (I918M)","short_name":"HPeV1-2A","sequence":"GPGSPYGQQPQNRMMKLAYLDRGFYKHYGIIVGDHVYQLDSDDIFKTALTGKAKFTKTKLTSDWVIEEECELDYFRIKYLESAVDSEHIFSVDKNCETIAKDIFGTHTLSQHQAIGLVGTILLTAGLMSTIKTPVNAVTIKEFFNHAMDGDEQ","organism":"Human parechovirus 1 (strain Harris)","uniprot_code":"Q66578","uniprot_range_first":777,"uniprot_range_last":923,"oligomerization":"dimer","molecular_type":"protein","uniprot_sequence":"METIKSIADMATGVVSSVDSTINAVNEKVESVGNEIGGNLLTKVADDASNILGPNCFATT\nAEPENKNVVQATTTVNTTNLTQHPSAPTMPFSPDFSNVDNFHSMAYDITTGDKNPSKLVR\nLETHEWTPSWARGYQITHVELPKVFWDHQDKPAYGQSRYFAAVRCGFHFQVQVNVNQGTA\nGSALVVYEPKPVVTYDSKLEFGAFTNLPHVLMNLAETTQADLCIPYVADTNYVKTDSSDL\nGQLKVYVWTPLSIPTGSANQVDVTILGSLLQLDFQNPRVFAQDVNIYDNAPNGKKKNWKK\nIMTMSTKYKWTRTKIDIAEGPGSMNMANVLCTTGAQSVALVGERAFYDPRTAGSKSRFDD\nLVKIAQLFSVMADSTTPSENHGVDAKGYFKWSATTAPQSIVHRNIVYLRLFPNLNVFVNS\nYSYFRGSLVLRLSVYASTFNRGRLRMGFFPNATTDSTSTLDNAIYTICDIGSDNSFEITI\nPYSFSTWMRKTNGHPIGLFQIEVLNRLTYNSSSPSEVYCIVQGKMGQDARFFCPTGSVVT\nFQNSWGSQMDLTDPLCIEDDTENCKQTMSPNELGLTSAQDDGPLGQEKPNYFLNFRSMNV\nDIFTVSHTKVDNLFGRAWFFMEHTFTNEGQWRVPLEFPKQGHGSLSLLFAYFTGELNIHV\nLFLSERGFLRVAHTYDTSNDRVNFLSSNGVITVPAGEQMTLSAPYYSNKPLRTVRDNNSL\nGYLMCKPFLTGTSTGKIEVYLSLRCPNFFFPLPAPKVTSSRALRGDMANLTNQSPYGQQP\nQNRMMKLAYLDRGFYKHYGIIVGDHVYQLDSDDIFKTALTGKAKFTKTKLTSDWVIEEEC\nELDYFRIKYLESAVDSEHIFSVDKNCETIAKDIFGTHTLSQHQAIGLVGTILLTAGLMST\nIKTPVNAVTIKEFFNHAIDGDEQGLSLLVQKCTTFFSSAATEILDNDLVKFIVKILVRIL\nCYMVLYCHKPNILTTACLSTLLIMDVTSSSVLSPSCKALMQCLMDGDVKKLAEIVAESMS\nNTDDDEVKEQICDTVKYTKTILSNQGPFKGFNEVSTAFRHIDWWIHTLLKIKDMVLSVFK\nPSIESKAIQWLERNKEHVCSILDYASDIIVESKDQSKMKTQDFYQRYSDCLAKFKPIMAI\nCFRSCHNSISNTVYRLFQELARIPNRISTNNDLIRIEPIGIWIQGEPGQGKSFLTHTLSR\nQLQKSCKLNGVFTNPTASEFMDGYDNQDIHLIDDLGQTRKEKDIEMLCNCISSVPFIVPM\nAHLEEKGKFYTSKLVVATTNKSDFSSTVLQDSGALKRRFPYIMHIRAAKAYSKAGKLNVS\nQAMATMSTGECWEVSKNGRDWETLKLKDLVDKITIDYNERVKNYNAWKQQLENQTLDDLD\nDAVSYIKHNFPDAIPYVDEYLNIEMSTLIEQMEAFIEPKPSVFKCFANKIGSKISKASRE\nVVDWFSDKIKSMLSFVERNKAWLTVVSAVTSAISILLLVTKIFKKEESKDERAYNPTLPV\nAKPKGTFPVSQREFKNEAPYDGQLEHIISQMAYITGSTTGHMTHCAGYQHDEIILHGHSI\nKYLEQEDELTLHYKNKVFPIEQPSVTQVTLGGKPMDLAILKCKLPFRFKKNSKYYTNKIG\nTESMLIWMTEQGIITKEVQRVHHSGGIKTREGTESTKTISYTVKSCKGMCGGLLISKVEG\nNFKILGMHIAGNGEMGVAIPFNFLKNDMSDQGIVTEITPIQPMYINTKTQIHKSPVYGAV\nEVKMGPAVLSKSDTRLEEPVECLIKKSASKYRVNKFQVNNELWQGVKACVKSKFREIFGM\nNGIVDMKTAILGTSHVNSMDLSTSAGYSFVKSGYKKKDLICLEPFSVAPLLERLVQDKFH\nNLLKGNQITTTFNTCLKDELRKLDKIASGKTRCIEACEVDYCIVYRMIMMEIYDKIYQTP\nCYYSGLAVGINPYKDWHFMINALNDYNYEMDYSQYDGSLSSMLLWEAVEVLAYCHDSPDL\nVMQLHKPVIDSDHVVFNERWLIHGGMPSGSPCTTVLNSLCNLMMCIYTTNLISPGIDCLP\nIVYGDDVILSLDKEIEPEKLQSIMADSFGAEVTGSRKDEPPSLKPRMEVEFLKRKPGYFP\nESTFIVGKLDTENMIQHLMWMKNFSTFKQQLQSYLMELCLHGKDTYQHYIKILEPYLQEW\nNITVDDYDVVITKLMPMVFD","mw":17.213,"total_mw":34.426,"number_molecules":2,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":"Human Parechovirus 1 2A protein from Genome polyprotein (I918M). 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":"Human Parechovirus 1 2A protein dimer 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/SASDUZ7_fit1_model1_img.png","software":"PyMOL","pdb_link":[{"pdb_code":"7ztw","ext_code":"7ZTW","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/SASDUZ7_fit1_model1.pdb","model_mw":32.12,"bead_radius":null,"log":"https://www.sasbdb.org/media/log_files/7ZTW_AB_Q8wVaA8.log","symmetry":null,"comment":"Chains A+B used for model fitting.","user":990}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDUZ7_fit1_fixed_fit_img.png","software":"CRYSOL","chi_square_value":0.986,"p_value":0.552,"fit_residual_plot":"SASDUZ7_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDUZ7_fit1.fit","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/7ZTW_AB_chromixs69cut_8a4TZiA.log","software_version":"crysol, ATSAS 3.2.1 (r14885)","description":""},{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDUZ7_fit2_model1_img.png","software":"SREFLEX","pdb_link":[],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDUZ7_fit2_model1.pdb","model_mw":32.04,"bead_radius":null,"log":null,"symmetry":null,"comment":"Model obtained from sReflex with 7ZTW Chains A+B as template","user":990}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDUZ7_fit2_fixed_fit_img.png","software":"SREFLEX","chi_square_value":0.962,"p_value":0.552,"fit_residual_plot":"SASDUZ7_fit2_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDUZ7_fit2.fit","fit_log":null,"software_version":"sreflex, ATSAS 3.2.1 (r14885)","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 HPeV1-2A (chains A+B) theoretical scattering curve was fitted to the experimental data using rigid body and normal mode analysis (SREFLEX). CAUTION: The monomer component of the models (16 kDa) does not include all of the amino acids of the protein construct used for SAXS (17.2 kDa).","experiment_description":"Synchrotron SAXS data from solutions of Human Parechovirus 1 2A protein dimer 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":33.1,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":36.15,"porod_mw_error":null,"pddf_i0":0.04674,"pddf_i0_error":null,"guinier_i0":0.0466741,"guinier_i0_error":null,"pddf_rg":2.262,"pddf_rg_error":null,"guinier_rg":2.24,"guinier_rg_error":0.004,"pddf_dmax":8.0,"pddf_dmax_error":null,"porod_volume":57.84,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":27,"guinier_point_last":337,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDUZ7_datloglog_img.png","symmetry":null,"last_modified":"2026-04-30T16:35:52.876292+02:00","bragg_peak":[]}