{ "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": [] }