{"code":"SASDG37","status":"Published","type_of_curve":"Single concentration","angular_unit":"1/nm","project":{"title":"Insights into herpesvirus assembly from the structure of the pUL7:pUL51 complex.","publication":{"title":"Insights into herpesvirus assembly from the structure of the pUL7:pUL51 complex.","author_list":"Butt BG, Owen DJ, Jeffries CM, Ivanova L, Hill CH, Houghton JW, Ahmed MF, Antrobus R, Svergun DI, Welch JJ, Crump CM, Graham SC","journal":"Elife","doi":"10.7554/eLife.53789","pmid":"32391791","published_date":"2020 May 11"},"status":"released","submitted_date":"2019-10-17","released_date":"2020-05-20"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDG37.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDG37.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG37_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG37_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDG37_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDG37_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDG37.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":"Tegument protein UL7","short_name":"pUL7","sequence":"MAAATADDEGSAATILKQAIAGDRSLVEAAEAISQQTLLRLACEVRQVGDRQPRFTATSIARVDVAPGCRLRFVLDGSPEDAYVTSEDYFKRCCGQSSYRGFAVAVLTANEDHVHSLAVPPLVLLHRFSLFNPRDLLDFELACLLMYLENCPRSHATPSTFAKVLAWLGVAGRRTSPFERVRCLFLRSCHWVLNTLMFMVHVKPFDDEFVLPHWYMARYLLANNPPPVLSALFCATPTSSSFRLPGPPPRSDCVAYNPAGIMGSCWASEEVRAPLVYWWLSETPKRQTSSLFYQFCGSLEVLFQ","organism":"Human alphaherpesvirus 1 strain KOS","uniprot_code":"A0A110B4Q7","uniprot_range_first":1,"uniprot_range_last":296,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MAAATADDEGSAATILKQAIAGDRSLVEAAEAISQQTLLRLACEVRQVGDRQPRFTATSI\nARVDVAPGCRLRFVLDGSPEDAYVTSEDYFKRCCGQSSYRGFAVAVLTANEDHVHSLAVP\nPLVLLHRFSLFNPRDLLDFELACLLMYLENCPRSHATPSTFAKVLAWLGVAGRRTSPFER\nVRCLFLRSCHWVLNTLMFMVHVKPFDDEFVLPHWYMARYLLANNPPPVLSALFCATPTSS\nSFRLPGPPPRSDCVAYNPAGIMGSCWASEEVRAPLVYWWLSETPKRQTSSLFYQFC","mw":33.907,"total_mw":33.907,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null},{"long_name":"Tegument protein UL51","short_name":"pUL51","sequence":"MISGWGARPEEQYEMIRAAVPPSEAEPRLQEALVVVNALLPAPITLDDALGSLDDTRRLVKARALARTYHACMVNLERLARHHPGLEAPTIDGAVAAHQDKMRRLADTCMATILQMYMSVGAADKSADVLVSQAIR","organism":"Human alphaherpesvirus 1 strain KOS","uniprot_code":"D3YPL0","uniprot_range_first":8,"uniprot_range_last":142,"oligomerization":"dimer","molecular_type":"protein","uniprot_sequence":"MASLLGAICGWGARPEEQYEMIRAAVPPSEAEPRLQEALVVVNALLPAPITLDDALGSLD\nDTRRLVKARALARTYHACMVNLERLARHHPGLEAPTIDGAVAAHQDKMRRLADTCMATIL\nQMYMSVGAADKSADVLVSQAIRSMAESDVVMEDVAIAERALGLSAFGVAGGTRSGGLGVT\nEAPSLGHPHTPPPEVTLAPAARNGDALPDPKPESCPRVSVPRPTASPTAPRPGPSRAAPC\nVLGQ","mw":14.814,"total_mw":29.628,"number_molecules":2,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null}],"buffer":{"name":"20 mM tris, 200 mM NaCl, 3% (v/v) glycerol, 0.25 mM TCEP","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":7.5,"deuteration":null},"purity_method":null,"name":"1:2 heterotrimer of pUL7 and pUL51(8-142) from herpes simplex virus 1","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":"University of Cambridge","webpage":null}],"contributor_name":"Benjamin","contributor_surname":"Butt","orcid":"https://orcid.org/0000-0001-6718-0470"}],"concentration_method":null,"concentration_unit":null,"date":"2019-05-16","storage_temperature":null,"cell_temperature":20.2,"exposure_time":0.995,"number_of_frames":3600,"wavelength":0.124,"sample_detector_distance":3.0,"concentration_min":null,"concentration_max":4.5,"sample_volume":null,"flow_rate":null,"s_min":0.079,"s_max":7.299,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDG37_fit1_model1_img.png","software":"DAMMIN","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":"SUPCOMB 23 (r9988)","model_data":"https://www.sasbdb.org/media/pdb_file/SASDG37_fit1_model1.pdb","model_mw":72.17,"bead_radius":2.5,"log":null,"symmetry":"P1","comment":"Refined DAMMIN model of the HSV-1 pUL7:pUL51(8-142) 1:2 heterotrimer","user":502}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDG37_fit1_fixed_fit_img.png","software":"DAMMIN","chi_square_value":1.04,"p_value":0.100571,"fit_residual_plot":"SASDG37_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDG37_fit1.fir","fit_log":null,"software_version":"5.3","description":"Fit of the refined DAMMIN model to the HSV-1 pUL7:pUL51 1:2 heterotrimer SAXS profile"},{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDG37_fit2_model1_img.png","software":"GASBOR","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDG37_fit2_model1.pdb","model_mw":null,"bead_radius":1.9,"log":null,"symmetry":"P1","comment":"Representative GASBOR model of the HSV-1 pUL7:pUL51(8-142) 1:2 heterotrimer","user":502}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDG37_fit2_fixed_fit_img.png","software":"GASBOR","chi_square_value":1.03,"p_value":0.161218,"fit_residual_plot":"SASDG37_fit2_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDG37_fit2.fir","fit_log":null,"software_version":"2.3i","description":"Fit of the representative GASBOR model to the HSV-1 pUL7:pUL51(8-142) heterotrimer SAXS profile"},{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDG37_fit3_model1_img.png","software":"CORAL","pdb_link":[{"pdb_code":"6t5a","ext_code":"6T5A","ext_type":"pdb","difference_with_model":"derived"}],"model_title":null,"type_of_model":"mix","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDG37_fit3_model1.pdb","model_mw":63.56,"bead_radius":1.9,"log":null,"symmetry":"P1","comment":null,"user":502}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDG37_fit3_fixed_fit_img.png","software":"CRYSOL","chi_square_value":1.034,"p_value":0.1398,"fit_residual_plot":"SASDG37_fit3_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDG37_fit3.fit","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/coral_100.log","software_version":null,"description":"CRYSOL fit of CORAL model"}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"5.0","i0_calibration_standard":null,"description":"The quoted experimental molecular mass, that corresponds to a 1:2 pUL7:pUL51(8-142) heterotrimer, was determined from SEC-MALLS-RI measurements performed on identical samples, eluted in parallel to the SEC-SAXS. The SEC-SAXS data for each individual run, Rg correlations through the main elution peak as well as the the SEC-MALLS-RI data and hydrodynamic estimates obtained from QELS are made available in the full-entry zip archive. The CORAL rigid-body refined (atomistic) model displayed in this entry is one example of several alternatives whereby a second copy of pUL51 samples different spatial positions bound within the complex. Additional representations of the 1:2 pUL7:pUL51(8-142) heterotrimeric complex, including those incorporating mass spectrometry cross-linking distance constraints, are also made available in the full entry zip-archive.","experiment_description":"Synchrotron SAXS data from the 1:2 heterotrimer of pUL7 and pUL51(8-142) from herpes simplex virus 1 in 20 mM tris, 200 mM NaCl, 3% (v/v) glycerol, 0.25 mM TCEP, pH 7.5 were collected on the EMBL P12 beam line at PETRA III (Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 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 profile displayed represents the average of three individual SEC-SAXS runs. The SEC parameters, per run, were as follows: A 75.00 μl sample at 4.5 mg/ml was injected at a 0.40 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 20°C. Approximately 100 successive 1 second frames were collected through the major SEC-elution peak and processed using CHROMIXS. 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":67.0,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":66.99,"porod_mw_error":null,"pddf_i0":3346.0,"pddf_i0_error":null,"guinier_i0":3331.04,"guinier_i0_error":2.09,"pddf_rg":3.023,"pddf_rg_error":null,"guinier_rg":2.96,"guinier_rg_error":0.01,"pddf_dmax":11.5,"pddf_dmax_error":null,"porod_volume":115.57,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":9,"guinier_point_last":131,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDG37_datloglog_img.png","symmetry":null,"last_modified":"2023-06-21T07:55:24.740692+02:00","bragg_peak":[]}