{ "code": "SASDVE8", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/A", "project": { "title": "Unraveling the molecular grammar and the structural transitions underlying the fibrillation of a viral fibrillogenic domain.", "publication": { "title": "Unraveling the molecular grammar and the structural transitions underlying the fibrillation of a viral fibrillogenic domain.", "author_list": "Gondelaud F, Leval J, Arora L, Walimbe A, Bignon C, Ptchelkine D, Brocca S, Mukhopadyay S, Longhi S", "journal": "Protein Sci", "doi": "10.1002/pro.70068", "pmid": "39985377", "published_date": "2025 Mar" }, "status": "released", "submitted_date": "2024-10-14", "released_date": "2025-02-24" }, "pddf_data": null, "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVE8.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVE8_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVE8_kratky_img.png", "pddf_plot": null, "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVE8_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVE8.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Eiger 4M", "resolution": 75.0 }, "name": "SOLEIL", "city": "Saint-Aubin", "country": "France", "beamline_name": "SWING", "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": "Protein W (artificial PNT3 variant - high-kappa)", "short_name": "PNT3 high K", "sequence": "MSYYHHHHHHLESTSLYKKAGFTPTEEPPVIPEYYYGSGDDGDLSESPPEGNVNLDSIEIYTSDDEDENQLEYEDEFAESSSEVVIDTTPEDNDSINQEEVVGDPSDQGLKHPFPLGKFPKKKRTPRVRRKRS", "organism": "Hendra virus (isolate Horse/Autralia/Hendra/1994)", "uniprot_code": "P0C1C6", "uniprot_range_first": 200, "uniprot_range_last": 310, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MDKLDLVNDGLDIIDFIQKNQKEIQKTYGRSSIQQPSTKDRTRAWEDFLQSTSGEHEQAE\r\nGGMPKNDGGTEGRNVEDLSSVTSSDGTIGQRVSNTRAWAEDPDDIQLDPMVTDVVYHDHG\r\nGECTGHGPSSSPERGWSYHMSGTHDGNVRAVPDTKVLPNAPKTTVPEEVREIDLIGLEDK\r\nFASAGLNPAAVPFVPKNQSTPTEEPPVIPEYYYGSGRRGDLSKSPPRGNVNLDSIKIYTS\r\nDDEDENQLEYEDEFAKSSSEVVIDTTPEDNDSINQEEVVGDPSDQGLEHPFPLGKFPEKE\r\nETPDVRRKDSLMQDSCKRGGVPKRLPMLSEEFECSGSDDPIIQELEREGSHPGGSLRLRE\r\nPPQSSGNSRNQPDRQLKTGDAASPGGVQRPGTPMPKSRIMPIKKGAQTRSLNMLGRKTCL\r\nGRRVVQPGMFADYPPTKKARVLLRRMSN", "mw": 15.198, "total_mw": 15.198, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "Artificial variant of PNT3 with a segregated distribution of the opposite charges (High kappa). The protein construct used for SAXS contains a non-native polyhistitine tag and additional amino acids (MSYYHHHHHHLESTSLYKKAGF)." } ], "buffer": { "name": "20 mM HEPES, 150 mM NaCl", "concentration_unit": null, "comment": "HBS", "additive": null, "concentration": null, "pka": null, "ph": 7.2, "deuteration": null }, "purity_method": null, "name": "Hendra virus protein P/V/W PNT3 high-K domain", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "13288 Marseille, France", "full_name": "CNRS, AFMB UMR 7257 ", "webpage": "" } ], "contributor_name": "Frank", "contributor_surname": "Gondelaud", "orcid": "" } ], "concentration_method": null, "concentration_unit": null, "date": "2024-04-05", "storage_temperature": 4.0, "cell_temperature": 20.0, "exposure_time": 0.99, "number_of_frames": 600, "wavelength": 0.133, "sample_detector_distance": 2.0, "concentration_min": null, "concentration_max": 5.0, "sample_volume": 50.0, "flow_rate": 0.3, "s_min": 0.089, "s_max": 4.689, "total_exposure_time": null, "seccolumn": 10 }, "fits": [ { "models": [], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVE8_fit1_fixed_fit_img.png", "software": "EOM/GAJOE", "chi_square_value": 1.006, "p_value": 0.1946, "fit_residual_plot": "SASDVE8_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVE8_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/logFile_001_1_nHnJcis.log", "software_version": null, "description": "EOM online was used." } ], "estimated_volume_method": null, "pddf_software": null, "pddf_software_version": null, "i0_calibration_standard": null, "description": "50 µl were injected on a BioSec 3-300 at 0.3 ml/min in HBS", "experiment_description": "Synchrotron SAXS data from solutions of Hendra virus protein P/V/W PNT3 high-K domain in 20 mM HEPES, 150 mM NaCl, pH 7.2 were collected on the SWING beam line at SOLEIL (Saint-Aubin, France) using a Eiger 4M detector at a sample-detector distance of 2 m and at a wavelength of λ = 0.133 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 50.00 μl sample at 5 mg/ml was injected at a 0.30 ml/min flow rate onto a Agilent Bio SEC-3, 300 Å column at 20°C. 600 successive 0.990 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": 23.3, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 33.6, "porod_mw_error": null, "pddf_i0": null, "pddf_i0_error": null, "guinier_i0": 1.10416, "guinier_i0_error": null, "pddf_rg": null, "pddf_rg_error": null, "guinier_rg": 3.126, "guinier_rg_error": 0.151, "pddf_dmax": 14.7, "pddf_dmax_error": null, "porod_volume": 53.8, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 51, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDVE8_datloglog_img.png", "symmetry": null, "last_modified": "2025-02-24T10:52:45.703208+01:00", "bragg_peak": [] }