{ "code": "SASDVB4", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/A", "project": { "title": "Bacterial targeting of the neutrophil inhibitory receptor LILRB3 to evade antibody immunity.", "publication": { "title": "Bacterial targeting of the neutrophil inhibitory receptor LILRB3 to evade antibody immunity.", "author_list": "Rumpret M, Lewis Marffy AL, Zhang Y, van Woudenbergh E, van der Lans SPA, Xu X, Fu Z, Zhao Y, Catton EA, Paré G, McGregor F, Spiller OB, Fernandes MJ, de Haas CJC, van Strijp JAG, van Sorge NM, Geisbrecht BV, McCarthy AJ", "journal": "Nat Commun", "doi": "10.1038/s41467-026-74098-6", "pmid": "42277001", "published_date": "2026 Jun 11" }, "status": "released", "submitted_date": "2024-07-11", "released_date": "2026-06-16" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDVB4.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVB4.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVB4_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVB4_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVB4_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVB4_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVB4.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "MAR 165 CCD", "resolution": null }, "name": "Advanced Light Source (ALS)", "city": "Berkeley, CA", "country": "USA", "beamline_name": "12.3.1 (SIBYLS)", "beam_geometry": "", "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": "Leukocyte immunoglobulin-like receptor subfamily B member 3 (P288R)", "short_name": "LILRB3", "sequence": "GPFPKPTLWAEPGSVISWGSPVTIWCQGSLEAQEYRLDKEGSPEPLDRNNPLEPKNKARFSIPSMTEHHAGRYRCHYYSSAGWSEPSDPLELVMTGFYNKPTLSALPSPVVASGGNMTLRCGSQKGYHHFVLMKEGEHQLPRTLDSQQLHSGGFQALFPVGPVNPSHRWRFTCYYYYMNTPQVWSHPSDPLEILPSGVSRKPSLLTLQGPVLAPGQSLTLQCGSDVGYDRFVLYKEGERDFLQRPGQQPQAGLSQANFTLGPVSRSHGGQYRCYGAHNLSSEWSAPSDPLNILMAGQIYDTVSLSAQPGPTVASGENVTLLCQSWWQFDTFLLTKEGAAHPPLRLRSMYGAHKYQAEFPMSPVTSAHAGTYRCYGSYSSNPHLLSFPSEPLELMVSGHSGGSSLPPTGPPSTPGLGRYLEHHHHHH", "organism": "Homo sapiens", "uniprot_code": "A0A0G2JM46", "uniprot_range_first": 24, "uniprot_range_last": 443, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MTPALTALLCLGLSLGPRTRVQAGPFPKPTLWAEPGSVISWGSPVTIWCQGSLEAQEYRL\nDKEGSPEPLDRNNPLEPKNKARFSIPSMTEHHAGRYRCHYYSSAGWSEPSDPLELVMTGF\nYNKPTLSALPSPVVASGGNMTLRCGSQKGYHHFVLMKEGEHQLPRTLDSQQLHSGGFQAL\nFPVGPVNPSHRWRFTCYYYYMNTPQVWSHPSDPLEILPSGVSRKPSLLTLQGPVLAPGQS\nLTLQCGSDVGYDRFVLYKEGERDFLQRPGQQPQAGLSQANFTLGPVSPSHGGQYRCYGAH\nNLSSEWSAPSDPLNILMAGQIYDTVSLSAQPGPTVASGENVTLLCQSWWQFDTFLLTKEG\nAAHPPLRLRSMYGAHKYQAEFPMSPVTSAHAGTYRCYGSYSSNPHLLSFPSEPLELMVSG\nHSGGSSLPPTGPPSTPGLGRYLEVLIGVSVAFVLLLFLLLFLLLRRQRHSKHRTSDQRKT\nDFQRPAGAAETEPKDRGLLRRSSPAADVQEENLYAAVKDTQSEDRVELDSQQSPHDEDPQ\nAVTYAPVKHSSPRREMASPPSSLSGEFLDTKDRQVEEDRQMDTEAAASEASQDVTYAQLH\nSLTLRRKATEPPPSQEGEPPAEPSIYATLAIH", "mw": 46.951, "total_mw": 46.951, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "The protein construct used for SAXS contains an additional non-native polyhistidine tag at the C-terminus (HHHHHH)." }, { "long_name": "IgA FC receptor (N770H)", "short_name": "B75KN-CTD", "sequence": "VEQDQPAPIPENSEMDQAKEKAKIAVSKYMSKVLDGVHQHLQKKNHSKIVDLFKELEAIKQQTIFDIDNAKTEVEIDNLVHDAFSKMNATVAKFQKGLETNT", "organism": "Streptococcus agalactiae", "uniprot_code": "P27951", "uniprot_range_first": 725, "uniprot_range_last": 826, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MFKSNYERKMRYSIRKFSVGVASVAVASLFMGSVAHASELVKDDSVKTTEVAAKPYPSMA\nQTDQGNNSSSSELETTKMEIPTTDIKKAVEPVEKTAGETSATDTGKREKQLQQWKNNLKN\nDVDNTILSHEQKNEFKTKIDETNDSDALLELENQFNETNRLLHIKQHEEVEKDKKAKQQK\nTLKQSDTKVDLSNIDKELNHQKSQVEKMAEQKGITNEDKDSMLKKIEDIRKQAQQADKKE\nDAEVKVREELGKLFSSTKAGLDQEIQEHVKKETSSEENTQKVDEHYANSLQNLAQKSLEE\nLDKATTNEQATQVKNQFLENAQKLKEIQPLIKETNVKLYKAMSESLEQVEKELKHNSEAN\nLEDLVAKSKEIVREYEGKLNQSKNLPELKQLEEEAHSKLKQVVEDFRKKFKTSEQVTPKK\nRVKRDLAANENNQQKIELTVSPENITVYEGEDVKFTVTAKSDSKTTLDFSDLLTKYNPSV\nSDRISTNYKTNTDNHKIAEITIKNLKLNESQTVTLKAKDDSGNVVEKTFTITVQKKEEKQ\nVPKTPEQKDSKTEEKVPQEPKSNDKNQLQELIKSAQQELEKLEKAIKELMEQPEIPSNPE\nYGIQKSIWESQKEPIQEAITSFKKIIGDSSSKYYTEHYFNKYKSDFMNYQLHAQMEMLTR\nKVVQYMNKYPDNAEIKKIFESDMKRTKEDNYGSLENDALKGYFEKYFLTPFNKIKQIVDD\nLDKKVEQDQPAPIPENSEMDQAKEKAKIAVSKYMSKVLDGVHQHLQKKNNSKIVDLFKEL\nEAIKQQTIFDIDNAKTEVEIDNLVHDAFSKMNATVAKFQKGLETNTPETPDTPKIPELPQ\nAPDTPQAPDTPHVPESPKAPEAPRVPESPKTPEAPHVPESPKAPEAPRVPESPKTPEAPH\nVPESPKTPEAPKIPEPPKTPDVPKLPDVPKLPDVPKLPDAPKLPDGLNKVGQAVFTSTDG\nNTKVTVVFDKPTDADKLHLKEVTTKELADKIAHKTGGGTVRVFDLSLSKGGKETHVNGER\nTVRLALGQTGSDVHVYHVKENGDLERIPSKVENGQVVFKTNHFSLFAIKTLSKDQNVTPP\nKQTKPSTQGSQVEIAESQTGKFQSKAANHKALATGNETVAKGNPTSTTEKKLPYTGVASN\nLVLEIMGLLGLIGTSFIAMKRRKS", "mw": 11.549, "total_mw": 11.549, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "" } ], "buffer": { "name": "20 mM HEPES, 300 mM NaCl", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.4, "deuteration": null }, "purity_method": null, "name": "β-Antigen C Protein B75KN-CTD domain bound to Leukocyte Immunoglobulin-Like Receptor LILR-B3", "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": "Kansas State University", "webpage": null } ], "contributor_name": "Ying", "contributor_surname": "Zhang", "orcid": "https://orcid.org/0009-0003-1603-7561" } ], "concentration_method": null, "concentration_unit": null, "date": "2023-11-17", "storage_temperature": 7.0, "cell_temperature": 4.0, "exposure_time": 2.0, "number_of_frames": 906, "wavelength": 0.1127, "sample_detector_distance": 2.1, "concentration_min": null, "concentration_max": 5.0, "sample_volume": 60.0, "flow_rate": 0.65, "s_min": 0.114, "s_max": 4.699, "total_exposure_time": null, "seccolumn": 40 }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVB4_fit1_model1_img.png", "software": "MultiFoXS", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDVB4_fit1_model1.pdb", "model_mw": 58.45, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 1086 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVB4_fit1_fixed_fit_img.png", "software": "FoXS", "chi_square_value": 1.020389, "p_value": 0.0, "fit_residual_plot": "SASDVB4_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVB4_fit1.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": "Size-exclusion chromatography coupled small-angle X-ray scattering (SEC-SAXS) data of B75KN-CTD bound to LILRB3 were obtained using the SIBYLS beamline 12.3.1 at the Advanced Light Source, Lawrence Berkeley National Laboratory. The experiments were conducted with a sample-to-detector distance of 2.1 m and a wavelength, λ, of 0.1127 nm, yielding scattering vectors (s) ranging from 0.1 nm⁻¹ to 4 nm⁻¹. The scattering vector, s, is calculated using the equation s = 4πsinθ/λ, where 2θ represents the scattering angle. Size-exclusion chromatography (SEC) was performed using an Agilent 1260 series HPLC with a Shodex analytical column. A 60 μl sample at a 5 mg/ml protein concentration was injected at a flow rate of 0.65 ml/min onto a Shodex KW-803 column at 4°C. A total of 906 successive 2-second frames were captured. Subsequently, data normalization was conducted against the intensity of the transmitted beam, followed by radial averaging, and subtraction of the scattering from a solvent blank.", "experiment_description": "-", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 77.5, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 109.0, "porod_mw_error": null, "pddf_i0": 72.09, "pddf_i0_error": null, "guinier_i0": 72.2953, "guinier_i0_error": null, "pddf_rg": 3.94, "pddf_rg_error": null, "guinier_rg": 3.906, "guinier_rg_error": 0.277, "pddf_dmax": 14.1, "pddf_dmax_error": null, "porod_volume": 175.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 2, "guinier_point_last": 43, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDVB4_datloglog_img.png", "symmetry": null, "last_modified": "2026-06-16T09:24:10.110652+02:00", "bragg_peak": [] }